Structure of PDB 4nd8 Chain C Binding Site BS01

Receptor Information
>4nd8 Chain C (length=477) Species: 354 (Azotobacter vinelandii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MSREEVESLIQEVLEVYPEKARKDRNKHLAVNDPAVTQSKKCIISNKKSQ
PGLMTIRGCAYAGSKGVVWGPIKDMIHISHGPVGCGQYSRAGRRNYYIGT
TGVNAFVTMNFTSDFQEKDIVFGGDKKLAKLIDEVETLFPLNKGISVQSE
CPIGLIGDDIESVSKVKGAELSKTIVPVRCEGFRGVSQSLGHHIANDAVR
DWVLGKRDEDTTFASTPYDVAIIGDYNIGGDAWSSRILLEEMGLRCVAQW
SGDGSISEIELTPKVKLNLVHCYRSMNYISRHMEEKYGIPWMEYNFFGPT
KTIESLRAIAAKFDESIQKKCEEVIAKYKPEWEAVVAKYRPRLEGKRVML
YIGGLRPRHVIGAYEDLGMEVVGTGYEFAHNDDYDRTMKEMGDSTLLYDD
VTGYEFEEFVKRIKPDLIGSGIKEKFIFQKMGIPFRQMHSWDYSGPYHGF
DGFAIFARDMDMTLNNPCWKKLQAPWE
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 chain4nd8 Chain C Residue 502 [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]
PDB4nd8 Turnover-Dependent Inactivation of the Nitrogenase MoFe-Protein at High pH.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		V70 R96 H195 Y229 I231 C275 S278 I355 G356 G357 L358 R359 F381 H442
Binding residue
(residue number reindexed from 1)		V67 R93 H192 Y226 I228 C272 S275 I352 G353 G354 L355 R356 F378 H439
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) C62 A65 R96 H195
Catalytic site (residue number reindexed from 1) C59 A62 R93 H192
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:4nd8, PDBe:4nd8, PDBj:4nd8
PDBsum4nd8
PubMed24392967
UniProtP07328|NIFD_AZOVI Nitrogenase molybdenum-iron protein alpha chain (Gene Name=nifD)

[Back to BioLiP]