MolNFT v1 · #168931 · protein

Vkor-like from takifugu rubripes

6WVI · Vitamin K epoxide reductase-like protein, termini…: “Vkor-like from takifugu rubripes”. X-ray diffraction, 1 ligand (CRO), 6 pockets (best druggability 0.78). MolNFT v1 #168931 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6WVI
Type: protein
Length: 411 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vitamin K epoxide reductase-like protein, termini restrained by green fluorescent protein
EC: 1.17.4.4
UniProt: P42212, Q6TEK8
Ligands: CRO
Pockets: 6 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vitamin K epoxide reductase-like protein, termini restrained by green fluorescent protein (EC 1.17.4.4)	protein	411	35% helix, 29% strand	P42212, Q6TEK8

Ligands and binding sites

CRO · {2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · chains A
OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · chains A

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

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	112	0.78	0.97	33	CRO
2	302	0.75	0.86	36	OLC
3	242	0.67	0.84	34	empty
4	181	0.48	0.76	39	empty
5	78	0.37	0.78	24	empty

Modifications

Observed in the structure: 2 cofactor, 2 disulfide (chromophore, disulfide).

Compared structures

6WVI · VKOR-like from Takifugu rubripes · the same entry in another collection · chain A against A, TM-score 1.00
P42212 · AlphaFold monomer V2.0 prediction for green fluorescent protein (P42212) · a predicted model of the same protein · chain A against A, TM-score 0.55

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 P42212
Every structure of UniProt Q6TEK8
Elsewhere: RCSB PDB 6WVI · PDBe 6WVI · UniProt P42212 · UniProt Q6TEK8

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