MolNFT v1 · #111779 · protein

Active aurone synthase (polyphenol oxidase), copper B : sulfohistidine ~ 1.4 : 1

4Z0Y: “Active aurone synthase (polyphenol oxidase), copper B : sulfohistidine ~ 1.4 : 1”. X-ray diffraction, 1 ligand (CU), 12 pockets (best druggability 0.84). MolNFT v1 #111779 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4Z0Y
Type: protein
Length: 1,428 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aurone synthase
UniProt: A0A075DN54
Ligands: CU
Pockets: 12 · best druggability 0.84

Structure

x-ray diffraction · 5 distinct chains · 35% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Aurone synthase	protein	347	39% helix, 10% strand	A0A075DN54
E	Aurone synthase	protein	8	0% helix, 0% strand	A0A075DN54
F	Aurone synthase	protein	12	0% helix, 0% strand	A0A075DN54
G	Aurone synthase	protein	10	0% helix, 0% strand	A0A075DN54
H	Aurone synthase	protein	10	0% helix, 0% strand	A0A075DN54

Ligands and binding sites

CU · Copper (II) ion · metal · 8 copies · chains A, B, C, D
GOL · Glycerol · additive · 5 copies · chains A, C, B, D

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

Pockets

12 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	1175	0.84	0.85	122	GOL
2	526	0.72	0.81	60	empty
3	238	0.49	0.74	40	empty
4	148	0.45	0.76	35	empty
5	123	0.44	0.77	15	empty

Interfaces

10 interfaces between chains.

A–C · 693 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 493 Å² buried · 4 hydrogen bonds · protein-protein
F–D · 388 Å² buried · 2 hydrogen bonds · protein-protein
B–H · 362 Å² buried · 0 hydrogen bonds · protein-protein
B–F · 258 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 4 modified (disulfide, nonstandard).

Compared structures

4Z0Y · Active aurone synthase (polyphenol oxidase), copper B : sulfohistidine ~ 1.4 : 1 · 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 A0A075DN54
Elsewhere: RCSB PDB 4Z0Y · PDBe 4Z0Y · UniProt A0A075DN54

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