7SF2 | pdb_00007sf2

Crystal Structure of Beta-Galactosidase from Bacteroides cellulosilyticus

PDB DOI: https://doi.org/10.2210/pdb7SF2/pdb

Classification: HYDROLASE
Organism(s): Bacteroides cellulosilyticus DSM 14838
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-10-02 Released: 2021-11-03
Deposition Author(s): Kim, Y., Joachimiak, G., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.209 (Depositor), 0.210 (DCC)
R-Value Work:
0.182 (Depositor), 0.180 (DCC)
R-Value Observed:
0.183 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal Structure of Beta-Galactosidase from Bacteroides cellulosilyticus

Kim, Y., Joachimiak, G., Endres, M., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 414.81 kDa
Atom Count: 31,047
Modelled Residue Count: 3,515
Deposited Residue Count: 3,528
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl hydrolase family 2, sugar binding domain protein	A, B, C, D, E A, B, C, D, E, F	588	Bacteroides cellulosilyticus DSM 14838	Mutation(s): 0 Gene Names: BACCELL_01794
UniProt
Find proteins for E2NBY7 (Bacteroides cellulosilyticus DSM 14838) Explore E2NBY7 Go to UniProtKB: E2NBY7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	E2NBY7
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain CB [auth C] SDF format, chain DC [auth E] SDF format, chain FA [auth B] SDF format, chain L [auth A] SDF format, chain QB [auth D] SDF format, chain QC [auth F] MOL2 format, chain CB [auth C] MOL2 format, chain DC [auth E] MOL2 format, chain FA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain QB [auth D] MOL2 format, chain QC [auth F] mmCIF format, chain CB [auth C] mmCIF format, chain DC [auth E] mmCIF format, chain FA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain QB [auth D] mmCIF format, chain QC [auth F]	CB [auth C] DC [auth E] FA [auth B] L [auth A] QB [auth D] CB [auth C], DC [auth E], FA [auth B], L [auth A], QB [auth D], QC [auth F]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain CB [auth C] Focus chain DC [auth E] Focus chain FA [auth B] Focus chain L [auth A] Focus chain QB [auth D] Focus chain QC [auth F] Interactions & Density Focus chain CB [auth C] Focus chain DC [auth E] Focus chain FA [auth B] Focus chain L [auth A] Focus chain QB [auth D] Focus chain QC [auth F]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain AC [auth E] SDF format, chain IB [auth C] SDF format, chain IC [auth E] SDF format, chain JC [auth E] SDF format, chain OC [auth F] SDF format, chain TA [auth B] SDF format, chain VB [auth D] SDF format, chain ZA [auth C] SDF format, chain VC [auth F] MOL2 format, chain AC [auth E] MOL2 format, chain IB [auth C] MOL2 format, chain IC [auth E] MOL2 format, chain JC [auth E] MOL2 format, chain OC [auth F] MOL2 format, chain TA [auth B] MOL2 format, chain VB [auth D] MOL2 format, chain ZA [auth C] MOL2 format, chain VC [auth F] mmCIF format, chain AC [auth E] mmCIF format, chain IB [auth C] mmCIF format, chain IC [auth E] mmCIF format, chain JC [auth E] mmCIF format, chain OC [auth F] mmCIF format, chain TA [auth B] mmCIF format, chain VB [auth D] mmCIF format, chain ZA [auth C] mmCIF format, chain VC [auth F]	AC [auth E] IB [auth C] IC [auth E] JC [auth E] OC [auth F] AC [auth E], IB [auth C], IC [auth E], JC [auth E], OC [auth F], TA [auth B], VB [auth D], VC [auth F], ZA [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain AC [auth E] Focus chain IB [auth C] Focus chain IC [auth E] Focus chain JC [auth E] Focus chain OC [auth F] Focus chain TA [auth B] Focus chain VB [auth D] Focus chain VC [auth F] Focus chain ZA [auth C] Interactions & Density Focus chain AC [auth E] Focus chain IB [auth C] Focus chain IC [auth E] Focus chain JC [auth E] Focus chain OC [auth F] Focus chain TA [auth B] Focus chain VB [auth D] Focus chain VC [auth F] Focus chain ZA [auth C]
BME Query on BME Download Ideal Coordinates CCD File SDF format, chain RA [auth B] MOL2 format, chain RA [auth B] mmCIF format, chain RA [auth B]	RA [auth B]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain RA [auth B] Interactions & Density Focus chain RA [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain BA [auth B] SDF format, chain BC [auth E] SDF format, chain CA [auth B] SDF format, chain DB [auth C] SDF format, chain EB [auth C] SDF format, chain FB [auth C] SDF format, chain FC [auth E] SDF format, chain GA [auth B] SDF format, chain GB [auth C] SDF format, chain GC [auth E] SDF format, chain H [auth A] SDF format, chain HA [auth B] SDF format, chain HB [auth C] SDF format, chain I [auth A] SDF format, chain IA [auth B] SDF format, chain JA [auth B] SDF format, chain K [auth A] SDF format, chain KA [auth B] SDF format, chain LA [auth B] SDF format, chain M [auth A] SDF format, chain MA [auth B] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain OA [auth B] SDF format, chain OB [auth D] SDF format, chain P [auth A] SDF format, chain PB [auth D] SDF format, chain QA [auth B] SDF format, chain R [auth A] SDF format, chain RB [auth D] SDF format, chain RC [auth F] SDF format, chain S [auth A] SDF format, chain SA [auth B] SDF format, chain SB [auth D] SDF format, chain TB [auth D] SDF format, chain TC [auth F] SDF format, chain UB [auth D] SDF format, chain UC [auth F] SDF format, chain W [auth A] SDF format, chain XA [auth C] SDF format, chain YA [auth C] SDF format, chain BB [auth C] SDF format, chain CC [auth E] SDF format, chain EA [auth B] SDF format, chain EC [auth E] SDF format, chain HC [auth E] SDF format, chain MC [auth F] SDF format, chain NA [auth B] SDF format, chain NB [auth D] SDF format, chain PA [auth B] SDF format, chain PC [auth F] SDF format, chain Q [auth A] SDF format, chain SC [auth F] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain ZB [auth E] MOL2 format, chain AB [auth C] MOL2 format, chain BA [auth B] MOL2 format, chain BC [auth E] MOL2 format, chain CA [auth B] MOL2 format, chain DB [auth C] MOL2 format, chain EB [auth C] MOL2 format, chain FB [auth C] MOL2 format, chain FC [auth E] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth C] MOL2 format, chain GC [auth E] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain HB [auth C] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain OB [auth D] MOL2 format, chain P [auth A] MOL2 format, chain PB [auth D] MOL2 format, chain QA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain RB [auth D] MOL2 format, chain RC [auth F] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain SB [auth D] MOL2 format, chain TB [auth D] MOL2 format, chain TC [auth F] MOL2 format, chain UB [auth D] MOL2 format, chain UC [auth F] MOL2 format, chain W [auth A] MOL2 format, chain XA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain BB [auth C] MOL2 format, chain CC [auth E] MOL2 format, chain EA [auth B] MOL2 format, chain EC [auth E] MOL2 format, chain HC [auth E] MOL2 format, chain MC [auth F] MOL2 format, chain NA [auth B] MOL2 format, chain NB [auth D] MOL2 format, chain PA [auth B] MOL2 format, chain PC [auth F] MOL2 format, chain Q [auth A] MOL2 format, chain SC [auth F] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain ZB [auth E] mmCIF format, chain AB [auth C] mmCIF format, chain BA [auth B] mmCIF format, chain BC [auth E] mmCIF format, chain CA [auth B] mmCIF format, chain DB [auth C] mmCIF format, chain EB [auth C] mmCIF format, chain FB [auth C] mmCIF format, chain FC [auth E] mmCIF format, chain GA [auth B] mmCIF format, chain GB [auth C] mmCIF format, chain GC [auth E] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain HB [auth C] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain LA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain OB [auth D] mmCIF format, chain P [auth A] mmCIF format, chain PB [auth D] mmCIF format, chain QA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain RB [auth D] mmCIF format, chain RC [auth F] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain SB [auth D] mmCIF format, chain TB [auth D] mmCIF format, chain TC [auth F] mmCIF format, chain UB [auth D] mmCIF format, chain UC [auth F] mmCIF format, chain W [auth A] mmCIF format, chain XA [auth C] mmCIF format, chain YA [auth C] mmCIF format, chain BB [auth C] mmCIF format, chain CC [auth E] mmCIF format, chain EA [auth B] mmCIF format, chain EC [auth E] mmCIF format, chain HC [auth E] mmCIF format, chain MC [auth F] mmCIF format, chain NA [auth B] mmCIF format, chain NB [auth D] mmCIF format, chain PA [auth B] mmCIF format, chain PC [auth F] mmCIF format, chain Q [auth A] mmCIF format, chain SC [auth F] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain ZB [auth E]	AB [auth C] BA [auth B] BB [auth C] BC [auth E] CA [auth B] AB [auth C], BA [auth B], BB [auth C], BC [auth E], CA [auth B], CC [auth E], DB [auth C], EA [auth B], EB [auth C], EC [auth E], FB [auth C], FC [auth E], GA [auth B], GB [auth C], GC [auth E], H [auth A], HA [auth B], HB [auth C], HC [auth E], I [auth A], IA [auth B], JA [auth B], K [auth A], KA [auth B], LA [auth B], M [auth A], MA [auth B], MC [auth F], N [auth A], NA [auth B], NB [auth D], O [auth A], OA [auth B], OB [auth D], P [auth A], PA [auth B], PB [auth D], PC [auth F], Q [auth A], QA [auth B], R [auth A], RB [auth D], RC [auth F], S [auth A], SA [auth B], SB [auth D], SC [auth F], T [auth A], TB [auth D], TC [auth F], U [auth A], UB [auth D], UC [auth F], V [auth A], W [auth A], XA [auth C], YA [auth C], ZB [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AB [auth C] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain BC [auth E] Focus chain CA [auth B] Focus chain CC [auth E] Focus chain DB [auth C] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain EC [auth E] Focus chain FB [auth C] Focus chain FC [auth E] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain GC [auth E] Focus chain H [auth A] Focus chain HA [auth B] Focus chain HB [auth C] Focus chain HC [auth E] Focus chain I [auth A] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain MC [auth F] Focus chain N [auth A] Focus chain NA [auth B] Focus chain NB [auth D] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth D] Focus chain P [auth A] Focus chain PA [auth B] Focus chain PB [auth D] Focus chain PC [auth F] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RB [auth D] Focus chain RC [auth F] Focus chain S [auth A] Focus chain SA [auth B] Focus chain SB [auth D] Focus chain SC [auth F] Focus chain T [auth A] Focus chain TB [auth D] Focus chain TC [auth F] Focus chain U [auth A] Focus chain UB [auth D] Focus chain UC [auth F] Focus chain V [auth A] Focus chain W [auth A] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZB [auth E] Interactions & Density Focus chain AB [auth C] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain BC [auth E] Focus chain CA [auth B] Focus chain CC [auth E] Focus chain DB [auth C] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain EC [auth E] Focus chain FB [auth C] Focus chain FC [auth E] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain GC [auth E] Focus chain H [auth A] Focus chain HA [auth B] Focus chain HB [auth C] Focus chain HC [auth E] Focus chain I [auth A] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain MC [auth F] Focus chain N [auth A] Focus chain NA [auth B] Focus chain NB [auth D] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth D] Focus chain P [auth A] Focus chain PA [auth B] Focus chain PB [auth D] Focus chain PC [auth F] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RB [auth D] Focus chain RC [auth F] Focus chain S [auth A] Focus chain SA [auth B] Focus chain SB [auth D] Focus chain SC [auth F] Focus chain T [auth A] Focus chain TB [auth D] Focus chain TC [auth F] Focus chain U [auth A] Focus chain UB [auth D] Focus chain UC [auth F] Focus chain V [auth A] Focus chain W [auth A] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZB [auth E]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain J [auth A] SDF format, chain KB [auth C] SDF format, chain KC [auth E] SDF format, chain LB [auth C] SDF format, chain NC [auth F] SDF format, chain VA [auth B] SDF format, chain WB [auth D] SDF format, chain XB [auth D] SDF format, chain Y [auth A] SDF format, chain Z [auth A] SDF format, chain JB [auth C] SDF format, chain UA [auth B] SDF format, chain X [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain KB [auth C] MOL2 format, chain KC [auth E] MOL2 format, chain LB [auth C] MOL2 format, chain NC [auth F] MOL2 format, chain VA [auth B] MOL2 format, chain WB [auth D] MOL2 format, chain XB [auth D] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain JB [auth C] MOL2 format, chain UA [auth B] MOL2 format, chain X [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain KB [auth C] mmCIF format, chain KC [auth E] mmCIF format, chain LB [auth C] mmCIF format, chain NC [auth F] mmCIF format, chain VA [auth B] mmCIF format, chain WB [auth D] mmCIF format, chain XB [auth D] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain JB [auth C] mmCIF format, chain UA [auth B] mmCIF format, chain X [auth A]	DA [auth B] J [auth A] JB [auth C] KB [auth C] KC [auth E] DA [auth B], J [auth A], JB [auth C], KB [auth C], KC [auth E], LB [auth C], NC [auth F], UA [auth B], VA [auth B], WB [auth D], X [auth A], XB [auth D], Y [auth A], Z [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain DA [auth B] Focus chain J [auth A] Focus chain JB [auth C] Focus chain KB [auth C] Focus chain KC [auth E] Focus chain LB [auth C] Focus chain NC [auth F] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WB [auth D] Focus chain X [auth A] Focus chain XB [auth D] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain DA [auth B] Focus chain J [auth A] Focus chain JB [auth C] Focus chain KB [auth C] Focus chain KC [auth E] Focus chain LB [auth C] Focus chain NC [auth F] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WB [auth D] Focus chain X [auth A] Focus chain XB [auth D] Focus chain Y [auth A] Focus chain Z [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain G [auth A] SDF format, chain LC [auth F] SDF format, chain MB [auth D] SDF format, chain WA [auth C] SDF format, chain YB [auth E] MOL2 format, chain AA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain LC [auth F] MOL2 format, chain MB [auth D] MOL2 format, chain WA [auth C] MOL2 format, chain YB [auth E] mmCIF format, chain AA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain LC [auth F] mmCIF format, chain MB [auth D] mmCIF format, chain WA [auth C] mmCIF format, chain YB [auth E]	AA [auth B] G [auth A] LC [auth F] MB [auth D] WA [auth C] AA [auth B], G [auth A], LC [auth F], MB [auth D], WA [auth C], YB [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain G [auth A] Focus chain LC [auth F] Focus chain MB [auth D] Focus chain WA [auth C] Focus chain YB [auth E] Interactions & Density Focus chain AA [auth B] Focus chain G [auth A] Focus chain LC [auth F] Focus chain MB [auth D] Focus chain WA [auth C] Focus chain YB [auth E]