Structure of PDB 3pdi Chain C Binding Site BS02

Receptor Information
>3pdi Chain C (length=427) Species: 322710 (Azotobacter vinelandii DJ) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GCAKPKPGATDGGCSFDGAQIALLPVADVAHIVHGPIACAGSSWDNRGTR
SSGPDLYRIGMTTDLTENDVIMGRAEKRLFHAIRQAVESYSPPAVFVYNT
CVPALIGDDVDAVCKAAAERFGTPVIPVDSAGFYGTKNLGNRIAGEAMLK
YVIGTREPDPLPVGSERPGIRVHDVNLIGEYNIAGEFWHVLPLLDELGLR
VLCTLAGDARYREVQTMHRAEVNMMVCSKAMLNVARKLQETYGTPWFEGS
FYGITDTSQALRDFARLLDDPDLTARTEALIAREEAKVRAALEPWRARLE
GKRVLLYTGGVKSWSVVSALQDLGMKVVATGTKKSTEEDKARIRELMGDD
VKMLDEGNARVLLKTVDEYQADILIAGGRNMYTALKGRVPFLDINQEREF
GYAGYDGMLELVRQLCITLECPVWEAV
Ligand information
Ligand IDCZL
InChIInChI=1S/8Fe.6HS.3S/h;;;;;;;;6*1H;;;
InChIKeyFRFZBLMXGBLMJN-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0S1[Fe]234[S@H]5[Fe]2678[Fe]592[S@H]3[Fe]493(S26)S[Fe]3234[Fe]1156[Fe]722(S8)[S@@H]1[Fe]5([S@@H]63)S24
OpenEye OEToolkits 1.7.0S1[Fe]234S5[Fe]2678[Fe]592S3[Fe]493(S26)S[Fe]3234[Fe]1156[Fe]722(S8)S1[Fe]5(S63)S24
CACTVS 3.370S1[Fe]|23|4|5[SH]6[Fe]|78|2[SH]3[Fe]9%10|4S[Fe]|%11|%12%13%14[SH]%15[Fe]1%16|5|%11[SH]%17[Fe]|%18|%12%16(S[Fe]6|79|%18[SH]8%10)[SH]%13[Fe]%14%15%17
CACTVS 3.370S1[Fe]|23|4|5[SH]6[Fe]|78|2[SH]3[Fe]9%10|4S[Fe]|%11|%12%13%14[SH]%15[Fe]1%16|5|%11[SH]%17[Fe]|%18|%12%16(S[Fe]6|79|%18[SH]8%10)[SH]%13[Fe@@]%14%15%17
FormulaFe8 H6 S9
NameL-Cluster (Fe8S9)
ChEMBL
DrugBank
ZINC
PDB chain3pdi Chain C Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3pdi Structure of Precursor-Bound NifEN: A Nitrogenase FeMo Cofactor Maturase/Insertase.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		N161 R165 T359 E360 E361
Binding residue
(residue number reindexed from 1)		N138 R142 T336 E337 E338
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) C37 D40 R70 N164
Catalytic site (residue number reindexed from 1) C14 D17 R47 N141
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0016163 nitrogenase activity
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0009399 nitrogen fixation
GO:0065003 protein-containing complex assembly

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3pdi, PDBe:3pdi, PDBj:3pdi
PDBsum3pdi
PubMed21212358
UniProtC1DH03

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