Structure of PDB 5vq3 Chain B

Receptor sequence

>5vq3B (length=458) Species: 1501 (Clostridium pasteurianum)

MLDATPKEIVERKALRINPAKTCQPVGAMYAALGIHNCLPHSHGSQGCCS
YHRTVLSRHFKEPAMASTSSFTEGASVFGGGSNIKTAVKNIFSLYNPDII
AVHTTCLSETLGDDLPTYISQMEDAGSIPEGKLVIHTNTPSYVGSHVTGF
ANMVQGIVNYLSENTGAKNGKINVIPGFVGPADMREIKRLFEAMDIPYIM
FPDTSGVLDGPTTGEYKMYPEGGTKIEDLKDTGNSDLTLSLGSYASDLGA
KTLEKKCKVPFKTLRTPIGVSATDEFIMALSEATGKEVPASIEEERGQLI
DLMIDAQQYLQGKKVALLGDPDEIIALSKFIIELGAIPKYVVTGTPGMKF
QKEIDAMLAEAGIEGSKVKVEGDFFDVHQWIKNEGVDLLISNTYGKFIAR
EENIPFVRFGFPIMDRYGHYYNPKVGYKGAIRLVEEITNVILDKIERECT
EEDFEVVR

3D structure

• PDB: 5vq3 Reversible Protonated Resting State of the Nitrogenase Active Site.
• Chain: B
• Resolution: 1.72 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	CLF	B	C23 S45 G47 C48 Y51 H52 T105 C106 S141	C23 S45 G47 C48 Y51 H52 T105 C106 S141
BS02	FE2	B	D301 D305	D301 D305
BS03	FE2	B	K61 E62	K61 E62

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:5vq3, PDBe:5vq3, PDBj:5vq3
• PDBsum: 5vq3
• PubMed: 28692802
• UniProt: P11347|NIFK_CLOPA Nitrogenase molybdenum-iron protein beta chain (Gene Name=nifK)