MolNFT v1 · #82373 · protein

Assimilatory nitrite reductase (NII3) - NH2OH complex from tobbaco leaf

3VKT: “Assimilatory nitrite reductase (NII3) - NH2OH complex from tobbaco leaf”. X-ray diffraction, 5 ligands (SRM, SF4, HOA), 4 pockets (best druggability 0.78). MolNFT v1 #82373 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 3VKT
Type: protein
Length: 538 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nitrite reductase
EC: 1.7.7.1
UniProt: Q76KB0
Ligands: SRM, SF4, HOA, K, CL
Pockets: 4 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nitrite reductase (EC 1.7.7.1)	protein	538	38% helix, 23% strand	Q76KB0

Ligands and binding sites

SRM · Siroheme · ligand · chains A
SF4 · Iron/sulfur cluster · ligand · chains A
HOA · Hydroxyamine · ligand · chains A
K · Potassium ion · metal · chains A
CL · Chloride ion · ion · 2 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	651	0.78	0.84	66	SRM, SF4, CL, HOA
2	228	0.58	0.79	34	empty
3	111	0.41	0.76	22	empty
4	84	0.36	0.76	14	empty

Compared structures

3VKT · Assimilatory nitrite reductase (Nii3) - NH2OH complex from tobbaco leaf · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q76KB0
Elsewhere: RCSB PDB 3VKT · PDBe 3VKT · UniProt Q76KB0

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