4V7M

The structures of Capreomycin bound to the 70S ribosome.

• PDB DOI: https://doi.org/10.2210/pdb4V7M/pdb
• Entry: 4V7M supersedes: 3KNL, 3KNM, 3KNN, 3KNO
• NAKB: 4V7M

• Classification: RIBOSOME/ANTIBIOTIC
• Organism(s): Thermus thermophilus HB8, Escherichia coli DH1, Pectobacterium parmentieri WPP163, Streptomyces californicus
• Expression System: Escherichia coli K-12, Escherichia coli HB101
• Mutation(s): No 


• Deposited: 2009-11-12 Released: 2014-07-09 
• Deposition Author(s): Stanley, R.E., Blaha, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free: 0.268 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 

Literature

The structures of the anti-tuberculosis antibiotics viomycin and capreomycin bound to the 70S ribosome.

Stanley, R.E., Blaha, G., Grodzicki, R.L., Strickler, M.D., Steitz, T.A.

(2010) Nat Struct Mol Biol 17: 289-293

• PubMed: 20154709 
• DOI: https://doi.org/10.1038/nsmb.1755
• Primary Citation of Related Structures:  
  4V7L, 4V7M


• PubMed Abstract: 
  

  Viomycin and capreomycin belong to the tuberactinomycin family of antibiotics, which are among the most effective antibiotics against multidrug-resistant tuberculosis. Here we present two crystal structures of the 70S ribosome in complex with three tRNAs and bound to either viomycin or capreomycin at 3.3- and 3.5-A resolution, respectively. Both antibiotics bind to the same site on the ribosome, which lies at the interface between helix 44 of the small ribosomal subunit and helix 69 of the large ribosomal subunit. The structures of these complexes suggest that the tuberactinomycins inhibit translocation by stabilizing the tRNA in the A site in the pretranslocation state. In addition, these structures show that the tuberactinomycins bind adjacent to the binding sites for the paromomycin and hygromycin B antibiotics, which may enable the development of new derivatives of tuberactinomycins that are effective against drug-resistant strains.

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Organizational Affiliation: 

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 51-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1v1w1x1y1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 51-mer - A2B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1v1w1x1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 51-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1v1w1x1y1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 51-mer - A2B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1v1w1x1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 4,566.15 kDa 
• Atom Count: 293,848 
• Modelled Residue Count: 21,190 
• Deposited Residue Count: 22,202 
• Unique protein chains: 51
• Unique nucleic acid chains: 8

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S2	B [auth AB], HB [auth CB]	256	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80371 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80371  Go to UniProtKB:  P80371

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S3	C [auth AC], IB [auth CC]	239	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80372 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80372  Go to UniProtKB:  P80372

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S4	D [auth AD], JB [auth CD]	209	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80373 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80373  Go to UniProtKB:  P80373

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S5	E [auth AE], KB [auth CE]	162	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHQ5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHQ5  Go to UniProtKB:  Q5SHQ5

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S6	F [auth AF], LB [auth CF]	101	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SLP8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLP8  Go to UniProtKB:  Q5SLP8

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S7	G [auth AG], MB [auth CG]	156	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P17291 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P17291  Go to UniProtKB:  P17291

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S8	H [auth AH], NB [auth CH]	138	Thermus thermophilus HB8	Mutation(s): 0

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S9	I [auth AI], OB [auth CI]	128	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80374 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80374  Go to UniProtKB:  P80374

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S10	J [auth AJ], PB [auth CJ]	105	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHN7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN7  Go to UniProtKB:  Q5SHN7

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S11	K [auth AK], QB [auth CK]	129	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80376 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80376  Go to UniProtKB:  P80376

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S12	L [auth AL], RB [auth CL]	132	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHN3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN3  Go to UniProtKB:  Q5SHN3

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S13	M [auth AM], SB [auth CM]	126	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80377 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80377  Go to UniProtKB:  P80377

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S14	N [auth AN], TB [auth CN]	61	Thermus thermophilus HB8	Mutation(s): 0

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S15	O [auth AO], UB [auth CO]	89	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SJ76 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJ76  Go to UniProtKB:  Q5SJ76

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S16	P [auth AP], VB [auth CP]	88	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SJH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJH3  Go to UniProtKB:  Q5SJH3

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S17	Q [auth AQ], WB [auth CQ]	105	Thermus thermophilus HB8	Mutation(s): 0

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S18	R [auth AR], XB [auth CR]	88	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SLQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLQ0  Go to UniProtKB:  Q5SLQ0

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S19	S [auth AS], YB [auth CS]	93	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP2  Go to UniProtKB:  Q5SHP2

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S20	T [auth AT], ZB [auth CT]	106	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80380 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80380  Go to UniProtKB:  P80380

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein Thx	AC [auth CU], U [auth AU]	27	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SIH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SIH3  Go to UniProtKB:  Q5SIH3

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
capreomycin IA	FC [auth CZ], Z [auth AZ]	6	Streptomyces californicus	Mutation(s): 0

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L1	CA [auth BC], IC [auth DC]	229	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SLP7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLP7  Go to UniProtKB:  Q5SLP7

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L2	DA [auth BD], JC [auth DD]	276	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60405 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60405  Go to UniProtKB:  P60405

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L3	EA [auth BE], KC [auth DE]	206	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHN8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN8  Go to UniProtKB:  Q5SHN8

Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L4	FA [auth BF], LC [auth DF]	210	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHN9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN9  Go to UniProtKB:  Q5SHN9

Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L5	GA [auth BG], MC [auth DG]	182	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHQ0  Go to UniProtKB:  Q5SHQ0

Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L6	HA [auth BH], NC [auth DH]	180	Thermus thermophilus HB8	Mutation(s): 0

Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L9	IA [auth BI], OC [auth DI]	148	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SLQ1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLQ1  Go to UniProtKB:  Q5SLQ1

Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L13	JA [auth BN], PC [auth DN]	140	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60488 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60488  Go to UniProtKB:  P60488

Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L14	KA [auth BO], QC [auth DO]	122	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP8  Go to UniProtKB:  Q5SHP8

Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L15	LA [auth BP], RC [auth DP]	150	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHQ7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHQ7  Go to UniProtKB:  Q5SHQ7

Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L16	MA [auth BQ], SC [auth DQ]	141	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60489 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60489  Go to UniProtKB:  P60489

Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L17	NA [auth BR], TC [auth DR]	118	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q9Z9H5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q9Z9H5  Go to UniProtKB:  Q9Z9H5

Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L18	OA [auth BS], UC [auth DS]	112	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHQ4 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHQ4  Go to UniProtKB:  Q5SHQ4

Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L19	PA [auth BT], VC [auth DT]	146	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60490 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60490  Go to UniProtKB:  P60490

Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L20	QA [auth BU], WC [auth DU]	118	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60491 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60491  Go to UniProtKB:  P60491

Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L21	RA [auth BV], XC [auth DV]	101	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60492 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60492  Go to UniProtKB:  P60492

Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L22	SA [auth BW], YC [auth DW]	113	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP3  Go to UniProtKB:  Q5SHP3

Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L23	TA [auth BX], ZC [auth DX]	96	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP0  Go to UniProtKB:  Q5SHP0

Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L24	AD [auth DY], UA [auth BY]	110	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP9  Go to UniProtKB:  Q5SHP9

Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L25	BD [auth DZ], VA [auth BZ]	206	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHZ1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHZ1  Go to UniProtKB:  Q5SHZ1

Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L27	CD [auth D0], WA [auth B0]	85	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60493 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60493  Go to UniProtKB:  P60493

Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L28	DD [auth D1], XA [auth B1]	98	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60494 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60494  Go to UniProtKB:  P60494

Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L29	ED [auth D2], YA [auth B2]	72	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP6  Go to UniProtKB:  Q5SHP6

Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L30	FD [auth D3], ZA [auth B3]	60	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHQ6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHQ6  Go to UniProtKB:  Q5SHQ6

Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L31	AB [auth B4], GD [auth D4]	71	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SJE1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJE1  Go to UniProtKB:  Q5SJE1

Entity ID: 54
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L32	BB [auth B5], HD [auth D5]	60	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80339 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80339  Go to UniProtKB:  P80339

Entity ID: 55
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L33	CB [auth B6], ID [auth D6]	54	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P35871 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P35871  Go to UniProtKB:  P35871

Entity ID: 56
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L34	DB [auth B7], JD [auth D7]	49	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80340 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80340  Go to UniProtKB:  P80340

Entity ID: 57
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L35	EB [auth B8], KD [auth D8]	65	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SKU1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKU1  Go to UniProtKB:  Q5SKU1

Entity ID: 58
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L36	FB [auth B9], LD [auth D9]	37	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHR2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHR2  Go to UniProtKB:  Q5SHR2

Entity ID: 1
Molecule	Chains	Length	Organism	Image
16S ribosomal RNA	A [auth AA], GB [auth CA]	1,508	Thermus thermophilus HB8

Entity ID: 22
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*AP*AP*AP*AP*AP*GP*GP*AP*AP*AP*UP*A*AP*AP*AP*AP*UP*GP*CP*AP*GP*UP*UP*CP*AP*AP*UP*CP*UP*A)-3')	BC [auth CV], V [auth AV]	30	N/A

Entity ID: 23
Molecule	Chains	Length	Organism	Image
tRNA-Gln	CC [auth CW], W [auth AW]	75	Escherichia coli DH1

Entity ID: 24
Molecule	Chains	Length	Organism	Image
tRNA-Met	X [auth AX]	77	Escherichia coli DH1

Entity ID: 25
Molecule	Chains	Length	Organism	Image
tRNA-Gln	EC [auth CY], Y [auth AY]	75	Pectobacterium parmentieri WPP163

Entity ID: 27
Molecule	Chains	Length	Organism	Image
23S ribosomal RNA	AA [auth BA], GC [auth DA]	2,915	Thermus thermophilus HB8

Entity ID: 28
Molecule	Chains	Length	Organism	Image
5S ribosomal RNA	BA [auth BB], HC [auth DB]	122	Thermus thermophilus HB8

Entity ID: 59
Molecule	Chains	Length	Organism	Image
RNA (77-MER)	DC [auth CX]	77	Escherichia coli DH1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	BKA [auth D5], BW [auth B4], DAA [auth CD], DKA [auth D9], DW [auth B5], EW [auth B9], WH [auth AD], ZJA [auth D4]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	AAA [auth CA], ABA [auth DA], ACA [auth DA], ADA [auth DA], AE [auth AA], AEA [auth DA], AF [auth AA], AFA [auth DA], AG [auth AA], AGA [auth DA], AH [auth AA], AHA [auth DA], AI [auth AW], AIA [auth DA], AJ [auth BA], AJA [auth DA], AK [auth BA], AKA [auth D5], AL [auth BA], AM [auth BA], AN [auth BA], AO [auth BA], AP [auth BA], AQ [auth BA], AR [auth BA], AS [auth BA], AT [auth BA], AU [auth BA], AV [auth BA], AW [auth B0], AX [auth CA], AY [auth CA], AZ [auth CA], BAA [auth CA], BBA [auth DA], BCA [auth DA], BDA [auth DA], BE [auth AA], BEA [auth DA], BF [auth AA], BFA [auth DA], BG [auth AA], BGA [auth DA], BH [auth AA], BHA [auth DA], BI [auth AW], BIA [auth DA], BJ [auth BA], BJA [auth DA], BK [auth BA], BL [auth BA], BM [auth BA], BN [auth BA], BO [auth BA], BP [auth BA], BQ [auth BA], BR [auth BA], BS [auth BA], BT [auth BA], BU [auth BA], BV [auth BA], BX [auth CA], BY [auth CA], BZ [auth CA], CAA [auth CA], CBA [auth DA], CCA [auth DA], CDA [auth DA], CE [auth AA], CEA [auth DA], CF [auth AA], CFA [auth DA], CG [auth AA], CGA [auth DA], CH [auth AA], CHA [auth DA], CI [auth AX], CIA [auth DA], CJ [auth BA], CJA [auth DA], CK [auth BA], CKA [auth D7], CL [auth BA], CM [auth BA], CN [auth BA], CO [auth BA], CP [auth BA], CQ [auth BA], CR [auth BA], CS [auth BA], CT [auth BA], CU [auth BA], CV [auth BA], CW [auth B5], CX [auth CA], CY [auth CA], CZ [auth CA], DBA [auth DA], DCA [auth DA], DDA [auth DA], DE [auth AA], DEA [auth DA], DF [auth AA], DFA [auth DA], DG [auth AA], DGA [auth DA], DH [auth AA], DHA [auth DA], DI [auth AX], DIA [auth DA], DJ [auth BA], DJA [auth DA], DK [auth BA], DL [auth BA], DM [auth BA], DN [auth BA], DO [auth BA], DP [auth BA], DQ [auth BA], DR [auth BA], DS [auth BA], DT [auth BA], DU [auth BA], DV [auth BA], DX [auth CA], DY [auth CA], DZ [auth CA], EAA [auth CE], EBA [auth DA], ECA [auth DA], EDA [auth DA], EE [auth AA], EEA [auth DA], EF [auth AA], EFA [auth DA], EG [auth AA], EGA [auth DA], EH [auth AA], EHA [auth DA], EI [auth AX], EIA [auth DA], EJ [auth BA], EJA [auth DA], EK [auth BA], EL [auth BA], EM [auth BA], EN [auth BA], EO [auth BA], EP [auth BA], EQ [auth BA], ER [auth BA], ES [auth BA], ET [auth BA], EU [auth BA], EV [auth BA], EX [auth CA], EY [auth CA], EZ [auth CA], FAA [auth CK], FBA [auth DA], FCA [auth DA], FDA [auth DA], FE [auth AA], FEA [auth DA], FF [auth AA], FFA [auth DA], FG [auth AA], FGA [auth DA], FH [auth AA], FHA [auth DA], FI [auth AX], FIA [auth DA], FJ [auth BA], FJA [auth DA], FK [auth BA], FL [auth BA], FM [auth BA], FN [auth BA], FO [auth BA], FP [auth BA], FQ [auth BA], FR [auth BA], FS [auth BA], FT [auth BA], FU [auth BA], FV [auth BA], FW [auth CA], FX [auth CA], FY [auth CA], FZ [auth CA], GAA [auth CV], GBA [auth DA], GCA [auth DA], GDA [auth DA], GE [auth AA], GEA [auth DA], GF [auth AA], GFA [auth DA], GG [auth AA], GGA [auth DA], GH [auth AA], GHA [auth DA], GI [auth AX], GIA [auth DA], GJ [auth BA], GJA [auth DA], GK [auth BA], GL [auth BA], GM [auth BA], GN [auth BA], GO [auth BA], GP [auth BA], GQ [auth BA], GR [auth BA], GS [auth BA], GT [auth BA], GU [auth BA], GV [auth BA], GW [auth CA], GX [auth CA], GY [auth CA], GZ [auth CA], HAA [auth CW], HBA [auth DA], HCA [auth DA], HDA [auth DA], HE [auth AA], HEA [auth DA], HF [auth AA], HFA [auth DA], HG [auth AA], HGA [auth DA], HH [auth AA], HHA [auth DA], HI [auth AX], HIA [auth DA], HJ [auth BA], HJA [auth DA], HK [auth BA], HL [auth BA], HM [auth BA], HN [auth BA], HO [auth BA], HP [auth BA], HQ [auth BA], HR [auth BA], HS [auth BA], HT [auth BA], HU [auth BA], HV [auth BB], HW [auth CA], HX [auth CA], HY [auth CA], HZ [auth CA], IAA [auth CW], IBA [auth DA], ICA [auth DA], IDA [auth DA], IE [auth AA], IEA [auth DA], IF [auth AA], IFA [auth DA], IG [auth AA], IGA [auth DA], IH [auth AA], IHA [auth DA], II [auth AX], IIA [auth DA], IJ [auth BA], IJA [auth DA], IK [auth BA], IL [auth BA], IM [auth BA], IN [auth BA], IO [auth BA], IP [auth BA], IQ [auth BA], IR [auth BA], IS [auth BA], IT [auth BA], IU [auth BA], IV [auth BB], IW [auth CA], IX [auth CA], IY [auth CA], IZ [auth CA], JAA [auth CW], JBA [auth DA], JCA [auth DA], JDA [auth DA], JE [auth AA], JEA [auth DA], JF [auth AA], JFA [auth DA], JG [auth AA], JGA [auth DA], JH [auth AA], JHA [auth DA], JI [auth AX], JIA [auth DA], JJ [auth BA], JJA [auth DA], JK [auth BA], JL [auth BA], JM [auth BA], JN [auth BA], JO [auth BA], JP [auth BA], JQ [auth BA], JR [auth BA], JS [auth BA], JT [auth BA], JU [auth BA], JV [auth BB], JW [auth CA], JX [auth CA], JY [auth CA], JZ [auth CA], KAA [auth CW], KBA [auth DA], KCA [auth DA], KDA [auth DA], KE [auth AA], KEA [auth DA], KF [auth AA], KFA [auth DA], KG [auth AA], KGA [auth DA], KH [auth AA], KHA [auth DA], KI [auth AX], KIA [auth DA], KJ [auth BA], KJA [auth DA], KK [auth BA], KL [auth BA], KM [auth BA], KN [auth BA], KO [auth BA], KP [auth BA], KQ [auth BA], KR [auth BA], KS [auth BA], KT [auth BA], KU [auth BA], KV [auth BB], KW [auth CA], KX [auth CA], KY [auth CA], KZ [auth CA], LAA [auth DA], LBA [auth DA], LCA [auth DA], LDA [auth DA], LE [auth AA], LEA [auth DA], LF [auth AA], LFA [auth DA], LG [auth AA], LGA [auth DA], LH [auth AA], LHA [auth DA], LI [auth BA], LIA [auth DA], LJ [auth BA], LJA [auth DA], LK [auth BA], LL [auth BA], LM [auth BA], LN [auth BA], LO [auth BA], LP [auth BA], LQ [auth BA], LR [auth BA], LS [auth BA], LT [auth BA], LU [auth BA], LV [auth BB], LW [auth CA], LX [auth CA], LY [auth CA], LZ [auth CA], MAA [auth DA], MBA [auth DA], MCA [auth DA], MD [auth AA], MDA [auth DA], ME [auth AA], MEA [auth DA], MF [auth AA], MFA [auth DA], MG [auth AA], MGA [auth DA], MH [auth AA], MHA [auth DA], MI [auth BA], MIA [auth DA], MJ [auth BA], MJA [auth DA], MK [auth BA], ML [auth BA], MM [auth BA], MN [auth BA], MO [auth BA], MP [auth BA], MQ [auth BA], MR [auth BA], MS [auth BA], MT [auth BA], MU [auth BA], MV [auth BD], MW [auth CA], MX [auth CA], MY [auth CA], MZ [auth CA], NAA [auth DA], NBA [auth DA], NCA [auth DA], ND [auth AA], NDA [auth DA], NE [auth AA], NEA [auth DA], NF [auth AA], NFA [auth DA], NG [auth AA], NGA [auth DA], NH [auth AA], NHA [auth DA], NI [auth BA], NIA [auth DA], NJ [auth BA], NJA [auth DA], NK [auth BA], NL [auth BA], NM [auth BA], NN [auth BA], NO [auth BA], NP [auth BA], NQ [auth BA], NR [auth BA], NS [auth BA], NT [auth BA], NU [auth BA], NV [auth BE], NW [auth CA], NX [auth CA], NY [auth CA], NZ [auth CA], OAA [auth DA], OBA [auth DA], OCA [auth DA], OD [auth AA], ODA [auth DA], OE [auth AA], OEA [auth DA], OF [auth AA], OFA [auth DA], OG [auth AA], OGA [auth DA], OH [auth AA], OHA [auth DA], OI [auth BA], OIA [auth DA], OJ [auth BA], OJA [auth DA], OK [auth BA], OL [auth BA], OM [auth BA], ON [auth BA], OO [auth BA], OP [auth BA], OQ [auth BA], OR [auth BA], OS [auth BA], OT [auth BA], OU [auth BA], OV [auth BE], OW [auth CA], OX [auth CA], OY [auth CA], OZ [auth CA], PAA [auth DA], PBA [auth DA], PCA [auth DA], PD [auth AA], PDA [auth DA], PE [auth AA], PEA [auth DA], PF [auth AA], PFA [auth DA], PG [auth AA], PGA [auth DA], PH [auth AA], PHA [auth DA], PI [auth BA], PIA [auth DA], PJ [auth BA], PJA [auth DA], PK [auth BA], PL [auth BA], PM [auth BA], PN [auth BA], PO [auth BA], PP [auth BA], PQ [auth BA], PR [auth BA], PS [auth BA], PT [auth BA], PU [auth BA], PV [auth BE], PW [auth CA], PX [auth CA], PY [auth CA], PZ [auth CA], QAA [auth DA], QBA [auth DA], QCA [auth DA], QD [auth AA], QDA [auth DA], QE [auth AA], QEA [auth DA], QF [auth AA], QFA [auth DA], QG [auth AA], QGA [auth DA], QH [auth AA], QHA [auth DA], QI [auth BA], QIA [auth DA], QJ [auth BA], QJA [auth DB], QK [auth BA], QL [auth BA], QM [auth BA], QN [auth BA], QO [auth BA], QP [auth BA], QQ [auth BA], QR [auth BA], QS [auth BA], QT [auth BA], QU [auth BA], QV [auth BF], QW [auth CA], QX [auth CA], QY [auth CA], QZ [auth CA], RAA [auth DA], RBA [auth DA], RCA [auth DA], RD [auth AA], RDA [auth DA], RE [auth AA], REA [auth DA], RF [auth AA], RFA [auth DA], RG [auth AA], RGA [auth DA], RH [auth AA], RHA [auth DA], RI [auth BA], RIA [auth DA], RJ [auth BA], RJA [auth DB], RK [auth BA], RL [auth BA], RM [auth BA], RN [auth BA], RO [auth BA], RP [auth BA], RQ [auth BA], RR [auth BA], RS [auth BA], RT [auth BA], RU [auth BA], RV [auth BG], RW [auth CA], RX [auth CA], RY [auth CA], RZ [auth CA], SAA [auth DA], SBA [auth DA], SCA [auth DA], SD [auth AA], SDA [auth DA], SE [auth AA], SEA [auth DA], SF [auth AA], SFA [auth DA], SG [auth AA], SGA [auth DA], SH [auth AA], SHA [auth DA], SI [auth BA], SIA [auth DA], SJ [auth BA], SJA [auth DB], SK [auth BA], SL [auth BA], SM [auth BA], SN [auth BA], SO [auth BA], SP [auth BA], SQ [auth BA], SR [auth BA], SS [auth BA], ST [auth BA], SU [auth BA], SV [auth BP], SW [auth CA], SX [auth CA], SY [auth CA], SZ [auth CA], TAA [auth DA], TBA [auth DA], TCA [auth DA], TD [auth AA], TDA [auth DA], TE [auth AA], TEA [auth DA], TF [auth AA], TFA [auth DA], TG [auth AA], TGA [auth DA], TH [auth AA], THA [auth DA], TI [auth BA], TIA [auth DA], TJ [auth BA], TJA [auth DD], TK [auth BA], TL [auth BA], TM [auth BA], TN [auth BA], TO [auth BA], TP [auth BA], TQ [auth BA], TR [auth BA], TS [auth BA], TT [auth BA], TU [auth BA], TV [auth BP], TW [auth CA], TX [auth CA], TY [auth CA], TZ [auth CA], UAA [auth DA], UBA [auth DA], UCA [auth DA], UD [auth AA], UDA [auth DA], UE [auth AA], UEA [auth DA], UF [auth AA], UFA [auth DA], UG [auth AA], UGA [auth DA], UH [auth AA], UHA [auth DA], UI [auth BA], UIA [auth DA], UJ [auth BA], UJA [auth DD], UK [auth BA], UL [auth BA], UM [auth BA], UN [auth BA], UO [auth BA], UP [auth BA], UQ [auth BA], UR [auth BA], US [auth BA], UT [auth BA], UU [auth BA], UV [auth BR], UW [auth CA], UX [auth CA], UY [auth CA], UZ [auth CA], VAA [auth DA], VBA [auth DA], VCA [auth DA], VD [auth AA], VDA [auth DA], VE [auth AA], VEA [auth DA], VF [auth AA], VFA [auth DA], VG [auth AA], VGA [auth DA], VH [auth AA], VHA [auth DA], VI [auth BA], VIA [auth DA], VJ [auth BA], VJA [auth DE], VK [auth BA], VL [auth BA], VM [auth BA], VN [auth BA], VO [auth BA], VP [auth BA], VQ [auth BA], VR [auth BA], VS [auth BA], VT [auth BA], VU [auth BA], VV [auth BU], VW [auth CA], VX [auth CA], VY [auth CA], VZ [auth CA], WAA [auth DA], WBA [auth DA], WCA [auth DA], WD [auth AA], WDA [auth DA], WE [auth AA], WEA [auth DA], WF [auth AA], WFA [auth DA], WG [auth AA], WGA [auth DA], WHA [auth DA], WI [auth BA], WIA [auth DA], WJ [auth BA], WJA [auth DF], WK [auth BA], WL [auth BA], WM [auth BA], WN [auth BA], WO [auth BA], WP [auth BA], WQ [auth BA], WR [auth BA], WS [auth BA], WT [auth BA], WU [auth BA], WV [auth BU], WW [auth CA], WX [auth CA], WY [auth CA], WZ [auth CA], XAA [auth DA], XBA [auth DA], XCA [auth DA], XD [auth AA], XDA [auth DA], XE [auth AA], XEA [auth DA], XF [auth AA], XFA [auth DA], XG [auth AA], XGA [auth DA], XH [auth AG], XHA [auth DA], XI [auth BA], XIA [auth DA], XJ [auth BA], XJA [auth DO], XK [auth BA], XL [auth BA], XM [auth BA], XN [auth BA], XO [auth BA], XP [auth BA], XQ [auth BA], XR [auth BA], XS [auth BA], XT [auth BA], XU [auth BA], XV [auth BX], XW [auth CA], XX [auth CA], XY [auth CA], XZ [auth CA], YAA [auth DA], YBA [auth DA], YCA [auth DA], YD [auth AA], YDA [auth DA], YE [auth AA], YEA [auth DA], YF [auth AA], YFA [auth DA], YG [auth AA], YGA [auth DA], YH [auth AW], YHA [auth DA], YI [auth BA], YIA [auth DA], YJ [auth BA], YJA [auth D0], YK [auth BA], YL [auth BA], YM [auth BA], YN [auth BA], YO [auth BA], YP [auth BA], YQ [auth BA], YR [auth BA], YS [auth BA], YT [auth BA], YU [auth BA], YV [auth B0], YW [auth CA], YX [auth CA], YY [auth CA], YZ [auth CA], ZAA [auth DA], ZBA [auth DA], ZCA [auth DA], ZD [auth AA], ZDA [auth DA], ZE [auth AA], ZEA [auth DA], ZF [auth AA], ZFA [auth DA], ZG [auth AA], ZGA [auth DA], ZH [auth AW], ZHA [auth DA], ZI [auth BA], ZIA [auth DA], ZJ [auth BA], ZK [auth BA], ZL [auth BA], ZM [auth BA], ZN [auth BA], ZO [auth BA], ZP [auth BA], ZQ [auth BA], ZR [auth BA], ZS [auth BA], ZT [auth BA], ZU [auth BA], ZV [auth B0], ZW [auth CA], ZX [auth CA], ZY [auth CA], ZZ [auth CA]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DPP	FC [auth CZ], Z [auth AZ]	L-PEPTIDE LINKING	C3 H8 N2 O2		ALA
KBE	FC [auth CZ], Z [auth AZ]	L-PEPTIDE LINKING	C6 H14 N2 O2		LYS
MYN	FC [auth CZ], Z [auth AZ]	L-PEPTIDE LINKING	C6 H12 N4 O2		ARG

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 26
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000193	FC [auth AZ], Z [auth CZ]	Capreomycin IA	Cyclic peptide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free: 0.268 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 210.355	α = 90
b = 448.236	β = 90
c = 631.156	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-09 
Deposition Author(s): Stanley, R.E., Blaha, G.
• This entry supersedes: 3KNL, 3KNM, 3KNN, 3KNO

Revision History  

• Version 1.0: 2014-07-09
  Type: Initial release
  
• Version 1.1: 2014-12-10
  Changes: Other
• Version 1.2: 2017-11-22
  Changes: Advisory, Refinement description