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Crystal structure of grenache (vitis vinifera) polyphenol oxidase

Analyse Crystal structure of grenache (vitis vinifera) polyphenol oxidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2P3X
Type: protein
Length: 339 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polyphenol oxidase, chloroplast
EC: 1.10.3.1
UniProt: P43311
Ligands: C2O
Pockets: 2 · best druggability 0.36

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Polyphenol oxidase, chloroplast (EC 1.10.3.1)	protein	339	38% helix, 9% strand	P43311

Ligands and binding sites

C2O · Cu-O-Cu linkage · ligand · chains A

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	95	0.36	0.75	25	empty
2	55	0.26	0.73	13	empty

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

2P3X · Crystal structure of Grenache (Vitis vinifera) Polyphenol Oxidase · the same entry in another collection · chain A against A, TM-score 1.00
P43311 · AlphaFold monomer V2.0 prediction for polyphenol oxidase, chloroplastic (P43311) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P43311
Elsewhere: RCSB PDB 2P3X · PDBe 2P3X · UniProt P43311

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