MolNFT v1 · #24931 · protein

Structure of the octameric flavoenzyme vanillyl-alcohol oxidase

1VAO: “Structure of the octameric flavoenzyme vanillyl-alcohol oxidase”. X-ray diffraction, 2 ligands (FAD, CL), 10 pockets (best druggability 0.87). MolNFT v1 #24931 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1VAO
Type: protein
Length: 1,100 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vanillyl-alcohol oxidase
EC: 1.1.3.13
UniProt: P56216
Ligands: FAD, CL
Pockets: 10 · best druggability 0.87

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Vanillyl-alcohol oxidase (EC 1.1.3.13)	protein	550	38% helix, 18% strand	P56216

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
CL · Chloride ion · ion · 2 copies · chains A, B
ACT · Acetate ion · additive · 2 copies · chains A, B

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

Pockets

10 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	660	0.87	0.92	80	ACT, CL, FAD
2	675	0.87	0.92	80	ACT, CL, FAD
3	1159	0.87	0.87	91	empty
4	54	0.48	0.85	16	empty
5	91	0.45	0.80	28	empty

Interfaces

1 interface between chains.

A–B · 4053 Å² buried · 48 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 cofactor (flavinylation).

Compared structures

1VAO · Structure of the octameric flavoenzyme vanillyl-alcohol oxidase · the same entry in another collection · chain A against A, TM-score 1.00
P56216 · AlphaFold monomer V2.0 prediction for vanillyl-alcohol oxidase (P56216) · a predicted model of the same protein · 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 P56216
Elsewhere: RCSB PDB 1VAO · PDBe 1VAO · UniProt P56216

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