Structure of PDB 3pdi Chain C Binding Site BS01

Receptor Information

>3pdi Chain C (length=427) Species: 322710 (Azotobacter vinelandii DJ)

GCAKPKPGATDGGCSFDGAQIALLPVADVAHIVHGPIACAGSSWDNRGTR
SSGPDLYRIGMTTDLTENDVIMGRAEKRLFHAIRQAVESYSPPAVFVYNT
CVPALIGDDVDAVCKAAAERFGTPVIPVDSAGFYGTKNLGNRIAGEAMLK
YVIGTREPDPLPVGSERPGIRVHDVNLIGEYNIAGEFWHVLPLLDELGLR
VLCTLAGDARYREVQTMHRAEVNMMVCSKAMLNVARKLQETYGTPWFEGS
FYGITDTSQALRDFARLLDDPDLTARTEALIAREEAKVRAALEPWRARLE
GKRVLLYTGGVKSWSVVSALQDLGMKVVATGTKKSTEEDKARIRELMGDD
VKMLDEGNARVLLKTVDEYQADILIAGGRNMYTALKGRVPFLDINQEREF
GYAGYDGMLELVRQLCITLECPVWEAV

Ligand information

• Ligand ID: SF4
• InChI: InChI=1S/4Fe.4S
• InChIKey: LJBDFODJNLIPKO-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: [S]12[Fe]3[S]4[Fe]1[S]5[Fe]2[S]3[Fe]45
  CACTVS 3.385: S1[Fe]S[Fe]1.S2[Fe]S[Fe]2
• Formula: Fe4 S4
• Name: IRON/SULFUR CLUSTER
• PDB chain: 3pdi Chain C Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3pdi Structure of Precursor-Bound NifEN: A Nitrogenase FeMo Cofactor Maturase/Insertase.
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): C37 C62 T123 C124 G155
• Binding residue (residue number reindexed from 1): C14 C39 T100 C101 G132
• Annotation score: 3

Enzymatic activity

• Catalytic site (original residue number in PDB): C37 D40 R70 N164
• Catalytic site (residue number reindexed from 1): C14 D17 R47 N141

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

External links

• PDB: RCSB:3pdi, PDBe:3pdi, PDBj:3pdi
• PDBsum: 3pdi
• PubMed: 21212358
• UniProt: C1DH03