Structure of PDB 5vpw Chain A Binding Site BS02

Receptor Information
>5vpw Chain A (length=517) Species: 1501 (Clostridium pasteurianum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NLKDEILEKYIPKTKKTRSGHIVIKTEETPNPEIVANTRTVPGIITARGC
AYAGCKGVVMGPIKDMVHITHGPIGCSFYTWGGRRFKSKPENGTGLNFNE
YVFSTDMQESDIVFGGVNKLKDAIHEAYEMFHPAAIGVYATCPVGLIGDD
ILAVAATASKEIGIPVHAFSCEGYKGVSQSAGHHIANNTVMTDIIGKGNK
EQKKYSINVLGEYNIGGDAWEMDRVLEKIGYHVNATLTGDATYEKVQNAD
KADLNLVQCHRSINYIAEMMETKYGIPWIKCNFIGVDGIVETLRDMAKCF
DDPELTKRTEEVIAEEIAAIQDDLDYFKEKLQGKTACLYVGGSRSHTYMN
MLKSFGVDSLVAGFEFAHRDDYEGREVIPTIKIDADSKNIPEITVTPDEQ
KYRVVIPEDKVEELKKAGVPLSSYGGMMKEMHDGTILIDDMNHHDMEVVL
EKLKPDMFFAGIKEKFVIQKGGVLSKQLHSYDYNGPYAGFRGVVNFGHEL
VNGIYTPAWKMITPPWK
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
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PDB5vpw Reversible Protonated Resting State of the Nitrogenase Active Site.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		C53 Y55 P76 G78 C79 T144 C145 G176
Binding residue
(residue number reindexed from 1)		C50 Y52 P73 G75 C76 T141 C142 G173
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) C53 A56 R87 H186
Catalytic site (residue number reindexed from 1) C50 A53 R84 H183
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5vpw, PDBe:5vpw, PDBj:5vpw
PDBsum5vpw
PubMed28692802
UniProtP00467|NIFD_CLOPA Nitrogenase molybdenum-iron protein alpha chain (Gene Name=nifD)

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