Structure of PDB 5n6y Chain D

Receptor sequence
>5n6yD (length=473) Species: 354 (Azotobacter vinelandii) [Search protein sequence]
PMVLLECDKDIPERQKHIYLKAPNEDTREFLPIANAATIPGTLSERGCAF
CGAKLVIGGVLKDTIQMIHGPLGCAYDTWHTKRYPTDNGHFNMKYVWSTD
MKESHVVFGGEKRLEKSMHEAFDEMPDIKRMIVYTTCPTALIGDDIKAVA
KKVMKDRPDVDVFTVECPGFSGVSQSKGHHVLNIGWINEKVETMEKEITS
EYTMNFIGDFNIQGDTQLLQTYWDRLGIQVVAHFTGNGTYDDLRCMHQAQ
LNVVNCARSSGYIANELKKRYGIPRLDIDSWGFNYMAEGIRKICAFFGIE
EKGEELIAEEYAKWKPKLDWYKERLQGKKMAIWTGGPRLWHWTKSVEDDL
GVQVVAMSSKFGHEEDFEKVIARGKEGTYYIDDGNELEFFEIIDLVKPDV
IFTGPRVGELVKKLHIPYVNGHGYHNGPYMGFEGFVNLARDMYNAVHNPL
RHLAAVDIRDKSQTTPVIVRGAA
3D structure
PDB5n6y The structure of vanadium nitrogenase reveals an unusual bridging ligand.
ChainD
Resolution1.35 Å
3D
structure
Catalytic site residues are labeled in the structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
Enzymatic activity
Catalytic site (original residue number in PDB) C49 C52 K83 H180
Catalytic site (residue number reindexed from 1) C48 C51 K82 H179
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 D C49 F51 P72 G74 C75 C138 G170 C48 F50 P71 G73 C74 C137 G169
BS02 8P8 D V57 K83 H180 F211 C257 S260 G336 P338 R339 F362 H423 V56 K82 H179 F210 C256 S259 G335 P337 R338 F361 H422
BS03 CO3 D T335 G336 G337 P338 R339 T334 G335 G336 P337 R338
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016163 nitrogenase activity
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
GO:0051212 vanadium ion binding
GO:0051536 iron-sulfur cluster binding
Biological Process
GO:0009399 nitrogen fixation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5n6y, PDBe:5n6y, PDBj:5n6y
PDBsum5n6y
PubMed28692069
UniProtP16855|VNFD_AZOVI Nitrogenase vanadium-iron protein alpha chain (Gene Name=vnfD)

[Back to BioLiP]