8TVT

Structure of human Cysteine desulfurase Nfs1 with L-propargylglycine bound to active site PLP in complex with ISD11, Acp1 and ISCU2

PDB DOI: https://doi.org/10.2210/pdb8TVT/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens, Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-08-18 Released: 2024-09-11
Deposition Author(s): Cygler, M., Boniecki, M.T.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.186
R-Value Work: 0.150
R-Value Observed: 0.152

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

D-Cysteine impairs tumor growth by inhibiting cysteine desulfurase NFS1

Zangari, J., Stehling, O., Freibert, S.A., Rouaud, F., Maundrell, K., Beinier, V.S., Ferre, M.S., Vartholomaiou, E., Montessuit, S., Schulz, V., Zuhra, K., Ruiz, V.G., Rudaz, S., Szabo, C., Hanschke, S., Tsukamoto, T., Boniecki, M.T., Cygler, M., Lill, R., Martinou, J.C.

To be published.

Macromolecule Content

Total Structure Weight: 84.14 kDa
Atom Count: 6,126
Modelled Residue Count: 684
Deposited Residue Count: 705
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine desulfurase	A	403	Homo sapiens	Mutation(s): 0 Gene Names: NFS1, NIFS, HUSSY-08 EC: 2.8.1.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y697 (Homo sapiens) Explore Q9Y697 Go to UniProtKB: Q9Y697
PHAROS: Q9Y697 GTEx: ENSG00000244005
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y697
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LYR motif-containing protein 4	B	91	Homo sapiens	Mutation(s): 1 Gene Names: LYRM4, C6orf149, ISD11, CGI-203
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HD34 (Homo sapiens) Explore Q9HD34 Go to UniProtKB: Q9HD34
PHAROS: Q9HD34 GTEx: ENSG00000214113
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9HD34
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl carrier protein	C	76	Escherichia coli	Mutation(s): 0 Gene Names: acpP
UniProt
Find proteins for A7ZKJ7 (Escherichia coli O139:H28 (strain E24377A / ETEC)) Explore A7ZKJ7 Go to UniProtKB: A7ZKJ7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A7ZKJ7
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Iron-sulfur cluster assembly enzyme ISCU	D	135	Homo sapiens	Mutation(s): 0 Gene Names: ISCU
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H1K1 (Homo sapiens) Explore Q9H1K1 Go to UniProtKB: Q9H1K1
PHAROS: Q9H1K1 GTEx: ENSG00000136003
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9H1K1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 13 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8Q1 Query on 8Q1 Download Ideal Coordinates CCD File SDF format, chain WA [auth C] MOL2 format, chain WA [auth C] mmCIF format, chain WA [auth C]	WA [auth C]	S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate C₂₃ H₄₅ N₂ O₈ P S MVHUOSAYFQKAMT-NRFANRHFSA-N		Interactions Focus chain WA [auth C] Interactions & Density Focus chain WA [auth C]
P15 Query on P15 Download Ideal Coordinates CCD File SDF format, chain Y [auth A] MOL2 format, chain Y [auth A] mmCIF format, chain Y [auth A]	Y [auth A]	2,5,8,11,14,17-HEXAOXANONADECAN-19-OL C₁₃ H₂₈ O₇ FHHGCKHKTAJLOM-UHFFFAOYSA-N		Interactions Focus chain Y [auth A] Interactions & Density Focus chain Y [auth A]
EDT Query on EDT Download Ideal Coordinates CCD File SDF format, chain UA [auth B] MOL2 format, chain UA [auth B] mmCIF format, chain UA [auth B]	UA [auth B]	{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID C₁₀ H₁₆ N₂ O₈ KCXVZYZYPLLWCC-UHFFFAOYSA-N		Interactions Focus chain UA [auth B] Interactions & Density Focus chain UA [auth B]
PLP (Subject of Investigation/LOI) Query on PLP Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain BB [auth D] MOL2 format, chain BB [auth D] mmCIF format, chain BB [auth D]	BB [auth D]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain BB [auth D] Interactions & Density Focus chain BB [auth D]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain XA [auth C] MOL2 format, chain XA [auth C] mmCIF format, chain XA [auth C]	XA [auth C]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain XA [auth C] Interactions & Density Focus chain XA [auth C]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain U [auth A] SDF format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A]	U [auth A], V [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain U [auth A] Focus chain V [auth A] Interactions & Density Focus chain U [auth A] Focus chain V [auth A]
DTT Query on DTT Download Ideal Coordinates CCD File SDF format, chain CA [auth A] MOL2 format, chain CA [auth A] mmCIF format, chain CA [auth A]	CA [auth A]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C₄ H₁₀ O₂ S₂ VHJLVAABSRFDPM-IMJSIDKUSA-N		Interactions Focus chain CA [auth A] Interactions & Density Focus chain CA [auth A]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain HA [auth A] MOL2 format, chain HA [auth A] mmCIF format, chain HA [auth A]	HA [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain HA [auth A] Interactions & Density Focus chain HA [auth A]
LPH (Subject of Investigation/LOI) Query on LPH Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	L-Propargylglycine C₅ H₇ N O₂ DGYHPLMPMRKMPD-BYPYZUCNSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain BA [auth A] SDF format, chain LA [auth A] SDF format, chain MA [auth A] SDF format, chain PA [auth B] SDF format, chain RA [auth B] SDF format, chain T [auth A] SDF format, chain W [auth A] SDF format, chain Z [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain RA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain W [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain RA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain W [auth A] mmCIF format, chain Z [auth A]	BA [auth A] LA [auth A] MA [auth A] PA [auth B] RA [auth B] BA [auth A], LA [auth A], MA [auth A], PA [auth B], RA [auth B], T [auth A], W [auth A], Z [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain BA [auth A] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain PA [auth B] Focus chain RA [auth B] Focus chain T [auth A] Focus chain W [auth A] Focus chain Z [auth A] Interactions & Density Focus chain BA [auth A] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain PA [auth B] Focus chain RA [auth B] Focus chain T [auth A] Focus chain W [auth A] Focus chain Z [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain CB [auth D] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain CB [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain CB [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	CB [auth D], I [auth A], J [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CB [auth D] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain CB [auth D] Focus chain I [auth A] Focus chain J [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain AB [auth D] SDF format, chain DA [auth A] SDF format, chain DB [auth D] SDF format, chain E [auth A] SDF format, chain EA [auth A] SDF format, chain F [auth A] SDF format, chain FA [auth A] SDF format, chain GA [auth A] SDF format, chain IA [auth A] SDF format, chain JA [auth A] SDF format, chain K [auth A] SDF format, chain KA [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth B] SDF format, chain O [auth A] SDF format, chain OA [auth B] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain SA [auth B] SDF format, chain TA [auth B] SDF format, chain VA [auth B] SDF format, chain X [auth A] SDF format, chain YA [auth C] SDF format, chain ZA [auth C] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth D] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth D] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain TA [auth B] MOL2 format, chain VA [auth B] MOL2 format, chain X [auth A] MOL2 format, chain YA [auth C] MOL2 format, chain ZA [auth C] mmCIF format, chain AA [auth A] mmCIF format, chain AB [auth D] mmCIF format, chain DA [auth A] mmCIF format, chain DB [auth D] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain TA [auth B] mmCIF format, chain VA [auth B] mmCIF format, chain X [auth A] mmCIF format, chain YA [auth C] mmCIF format, chain ZA [auth C]	AA [auth A] AB [auth D] DA [auth A] DB [auth D] E [auth A] AA [auth A], AB [auth D], DA [auth A], DB [auth D], E [auth A], EA [auth A], F [auth A], FA [auth A], GA [auth A], IA [auth A], JA [auth A], K [auth A], KA [auth A], L [auth A], M [auth A], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], Q [auth A], QA [auth B], R [auth A], S [auth A], SA [auth B], TA [auth B], VA [auth B], X [auth A], YA [auth C], ZA [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth D] Focus chain DA [auth A] Focus chain DB [auth D] Focus chain E [auth A] Focus chain EA [auth A] Focus chain F [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain K [auth A] Focus chain KA [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain S [auth A] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain VA [auth B] Focus chain X [auth A] Focus chain YA [auth C] Focus chain ZA [auth C] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth D] Focus chain DA [auth A] Focus chain DB [auth D] Focus chain E [auth A] Focus chain EA [auth A] Focus chain F [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain K [auth A] Focus chain KA [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain S [auth A] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain VA [auth B] Focus chain X [auth A] Focus chain YA [auth C] Focus chain ZA [auth C]