Structure of PDB 5vpw Chain D

Receptor sequence

>5vpwD (length=458) Species: 1501 (Clostridium pasteurianum)

MLDATPKEIVERKALRINPAKTCQPVGAMYAALGIHNCLPHSHGSQGCCS
YHRTVLSRHFKEPAMASTSSFTEGASVFGGGSNIKTAVKNIFSLYNPDII
AVHTTCLSETLGDDLPTYISQMEDAGSIPEGKLVIHTNTPSYVGSHVTGF
ANMVQGIVNYLSENTGAKNGKINVIPGFVGPADMREIKRLFEAMDIPYIM
FPDTSGVLDGPTTGEYKMYPEGGTKIEDLKDTGNSDLTLSLGSYASDLGA
KTLEKKCKVPFKTLRTPIGVSATDEFIMALSEATGKEVPASIEEERGQLI
DLMIDAQQYLQGKKVALLGDPDEIIALSKFIIELGAIPKYVVTGTPGMKF
QKEIDAMLAEAGIEGSKVKVEGDFFDVHQWIKNEGVDLLISNTYGKFIAR
EENIPFVRFGFPIMDRYGHYYNPKVGYKGAIRLVEEITNVILDKIERECT
EEDFEVVR

3D structure

• PDB: 5vpw Reversible Protonated Resting State of the Nitrogenase Active Site.
• Chain: D
• Resolution: 1.85 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): C106 T110
• Catalytic site (residue number reindexed from 1): C106 T110
• Enzyme Commision number: 1.18.6.1: nitrogenase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	FE2	D	K61 E62	K61 E62
BS02	FE2	D	D301 D305	D301 D305
BS03	CLF	D	C23 S45 G47 C48 Y51 H52 T105 C106 S141	C23 S45 G47 C48 Y51 H52 T105 C106 S141

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

External links

• PDB: RCSB:5vpw, PDBe:5vpw, PDBj:5vpw
• PDBsum: 5vpw
• PubMed: 28692802
• UniProt: P11347|NIFK_CLOPA Nitrogenase molybdenum-iron protein beta chain (Gene Name=nifK)