Structure of PDB 5xvb Chain M Binding Site BS02

Receptor Information
>5xvb Chain M (length=551) Species: 1080067 (Citrobacter sp. S-77) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SQRITIDPVTRIEGHLRIDCEIENGVVSKAWASGTMWRGMEEIVKNRDPR
DAWMIVQRICGVCTTTHAISSVRAAESALNIDVPVNAQYIRNIILAAHTT
HDHIVHFYQLSALDWVDITSALKADPAKASAMLNGVSTWHLNSAEEFTKV
QNKIKDLVASGQLGIFANGCWGHPAMQLPPEVNLIAVAHYLQALECQRDA
NRVVALLGGKTPHIQNLAVGGVANPINLDGLGVLNLERLMYIKSFIDKLS
DFVEQVYKVDTAVIAAFYPEWLERGQGAVNYLSAPEFPTDGKNGSFLFPG
GYITDADLSTYRPITSHSDEYLIKGIQESAKHAWYKDEAPQAPWEGTTVP
DYTGWSDDGKYSWVKAPTFYGKTVEVGPLANMLCKLAAKRESTHAKLNEI
VAIYTKLTGKTIEVAQLHSTLGRIIGRTVHCCELQNVLQDQYNALIVNIG
KGDHTTFVKPDIPATGEFKGVGFLEAPRGMLSHWMVIKDGIISNYQAVVP
STWNSGPRNFNDEVGPYERSLVGTPIADPNKPLEVVRTIHSFDPCMSCAV
H
Ligand information
Ligand IDNFU
InChIInChI=1S/2CN.CHO.Fe.Ni/c3*1-2;;/h;;1H;;
InChIKeyQCZROEOIPZWDEO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370[Ni]|[Fe](C=O)(C#N)C#N
ACDLabs 12.01N#C[Fe]([Ni])(C#N)C=O
OpenEye OEToolkits 1.7.0C(=O)[Fe](C#N)(C#N)[Ni]
FormulaC3 H Fe N2 Ni O
Nameformyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni);
NI-FE REDUCED ACTIVE CENTER
ChEMBL
DrugBank
ZINC
PDB chain5xvb Chain M Residue 602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5xvb Redox-dependent conformational changes of a proximal [4Fe-4S] cluster in Hyb-type [NiFe]-hydrogenase to protect the active site from O2.
Resolution1.84 Å
Binding residue
(original residue number in PDB)		C61 C64 H68 P478 R479 L482 V500 P501 S502 C546 C549
Binding residue
(residue number reindexed from 1)		C60 C63 H67 P477 R478 L481 V499 P500 S501 C545 C548
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) E14 C61 C64 H68 R479 S502 C546 C549
Catalytic site (residue number reindexed from 1) E13 C60 C63 H67 R478 S501 C545 C548
Enzyme Commision number 1.12.99.6: hydrogenase (acceptor).
Gene Ontology
Molecular Function
GO:0008901 ferredoxin hydrogenase activity
GO:0016151 nickel cation binding
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
Cellular Component
GO:0005886 plasma membrane

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:5xvb, PDBe:5xvb, PDBj:5xvb
PDBsum5xvb
PubMed30328414
UniProtA0A3B6UEP7

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