MolNFT v1 · #126553 · protein

Structure of recombinant mushroom tyrosinase (ABPPO4)

5M6B · Polyphenol oxidase 4: “Structure of recombinant mushroom tyrosinase (ABPPO4)”. X-ray diffraction, 2 ligands (CU, O), 20 pockets (best druggability 0.83). MolNFT v1 #126553 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5M6B
Type: protein
Length: 2,162 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polyphenol oxidase 4
EC: 1.14.18.1
UniProt: C7FF05
Ligands: CU, O
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 32% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Polyphenol oxidase 4 (EC 1.14.18.1)	protein	555	32% helix, 17% strand	C7FF05
A	Polyphenol oxidase 4 (EC 1.14.18.1)	protein	548	32% helix, 16% strand	C7FF05
C	Polyphenol oxidase 4 (EC 1.14.18.1)	protein	514	32% helix, 17% strand	C7FF05
D	Polyphenol oxidase 4 (EC 1.14.18.1)	protein	545	32% helix, 16% strand	C7FF05

Ligands and binding sites

CU · Copper (II) ion · metal · 8 copies · chains B, A, C, D
O · Oxygen atom · ion · chains A

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	692	0.83	0.87	93	empty
2	233	0.78	0.92	42	empty
3	260	0.78	0.90	36	empty
4	1000	0.75	0.78	75	empty
5	899	0.71	0.76	87	empty

Interfaces

5 interfaces between chains.

B–A · 1078 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 347 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 217 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 193 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 135 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5M6B · structure of recombinant mushroom tyrosinase (abPPO4) · the same entry in another collection · chain D against D, TM-score 1.00
C7FF05 · AlphaFold monomer V2.0 prediction for polyphenol oxidase 4 (C7FF05) · 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 C7FF05
Elsewhere: RCSB PDB 5M6B · PDBe 5M6B · UniProt C7FF05

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