Structure of PDB 5vpw Chain B Binding Site BS01

Receptor Information
>5vpw Chain B (length=458) Species: 1501 (Clostridium pasteurianum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLDATPKEIVERKALRINPAKTCQPVGAMYAALGIHNCLPHSHGSQGCCS
YHRTVLSRHFKEPAMASTSSFTEGASVFGGGSNIKTAVKNIFSLYNPDII
AVHTTCLSETLGDDLPTYISQMEDAGSIPEGKLVIHTNTPSYVGSHVTGF
ANMVQGIVNYLSENTGAKNGKINVIPGFVGPADMREIKRLFEAMDIPYIM
FPDTSGVLDGPTTGEYKMYPEGGTKIEDLKDTGNSDLTLSLGSYASDLGA
KTLEKKCKVPFKTLRTPIGVSATDEFIMALSEATGKEVPASIEEERGQLI
DLMIDAQQYLQGKKVALLGDPDEIIALSKFIIELGAIPKYVVTGTPGMKF
QKEIDAMLAEAGIEGSKVKVEGDFFDVHQWIKNEGVDLLISNTYGKFIAR
EENIPFVRFGFPIMDRYGHYYNPKVGYKGAIRLVEEITNVILDKIERECT
EEDFEVVR
Ligand information
Ligand IDCLF
InChIInChI=1S/8Fe.7S
InChIKeyJKVMXLBGZBULKV-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7[S]12[Fe]3[S]4[Fe]1S567([Fe]2[S]3[Fe]45)[Fe]8[S]9[Fe]6[S]1[Fe]9[S]8[Fe]71
CACTVS 3.385S1[Fe]S[Fe]2S[Fe][S]234([Fe]1)[Fe]S[Fe]S[Fe]3S[Fe]4
FormulaFe8 S7
NameFE(8)-S(7) CLUSTER
ChEMBL
DrugBank
ZINC
PDB chain5vpw Chain A Residue 603 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5vpw Reversible Protonated Resting State of the Nitrogenase Active Site.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		C23 S45 G47 C48 Y51 H52 T105 C106 S141
Binding residue
(residue number reindexed from 1)		C23 S45 G47 C48 Y51 H52 T105 C106 S141
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) C106 T110
Catalytic site (residue number reindexed from 1) C106 T110
Enzyme Commision number 1.18.6.1: nitrogenase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016163 nitrogenase activity
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
GO:0051536 iron-sulfur cluster binding
Biological Process
GO:0009399 nitrogen fixation
Cellular Component
GO:0016612 molybdenum-iron nitrogenase complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5vpw, PDBe:5vpw, PDBj:5vpw
PDBsum5vpw
PubMed28692802
UniProtP11347|NIFK_CLOPA Nitrogenase molybdenum-iron protein beta chain (Gene Name=nifK)

[Back to BioLiP]