Structure of PDB 5vpw Chain A Binding Site BS01

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 IDICS
InChIInChI=1S/C.7Fe.Mo.9S
InChIKeyDDQFAOMIVKLFON-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370S1|2[Fe]|3S4|[Fe]15S[Fe]67S|8[Mo]9|S%10[Fe]%11|8S[Fe]%12|2S|3[Fe]4%13S[Fe]%10(|S69)[C]57%11%12%13
OpenEye OEToolkits 1.7.2C12345[Fe]67S[Fe]18[S]9[Fe]21S[Fe]32[S]6[Fe]3[S]7[Fe]4([S]23)S[Fe]52[S]8[Mo]9[S]12
FormulaC Fe7 Mo S9
Nameiron-sulfur-molybdenum cluster with interstitial carbon
ChEMBL
DrugBank
ZINC
PDB chain5vpw Chain A Residue 602 [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)		V61 R87 H186 C262 S265 G344 G345 S346 R347 F369 H482
Binding residue
(residue number reindexed from 1)		V58 R84 H183 C259 S262 G341 G342 S343 R344 F366 H479
Annotation score2
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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