MolNFT v1 · #111785 · protein

Recombinantly expressed latent aurone synthase (polyphenol oxidase)

4Z14: “Recombinantly expressed latent aurone synthase (polyphenol oxidase)”. X-ray diffraction, 1 ligand (CU), 20 pockets (best druggability 0.83). MolNFT v1 #111785 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4Z14
Type: protein
Length: 4,007 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aurone synthase
UniProt: A0A075DN54
Ligands: CU
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 8 distinct chains · 27% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D	Aurone synthase	protein	501	28% helix, 20% strand	A0A075DN54
B	Aurone synthase	protein	504	26% helix, 19% strand	A0A075DN54
H	Aurone synthase	protein	498	28% helix, 20% strand	A0A075DN54
F	Aurone synthase	protein	498	28% helix, 20% strand	A0A075DN54
C	Aurone synthase	protein	499	26% helix, 20% strand	A0A075DN54
E	Aurone synthase	protein	497	26% helix, 20% strand	A0A075DN54
G	Aurone synthase	protein	509	27% helix, 19% strand	A0A075DN54
A	Aurone synthase	protein	501	27% helix, 19% strand	A0A075DN54

Ligands and binding sites

CU · Copper (II) ion · metal · 16 copies · chains D, B, H, F, C, E, G, 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, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	782	0.83	0.87	73	empty
2	987	0.83	0.85	82	empty
3	862	0.83	0.85	64	empty
4	859	0.80	0.83	89	empty
5	780	0.78	0.82	55	empty

Interfaces

13 interfaces between chains.

C–E · 746 Å² buried · 14 hydrogen bonds · protein-protein
D–F · 723 Å² buried · 12 hydrogen bonds · protein-protein
B–H · 711 Å² buried · 14 hydrogen bonds · protein-protein
D–H · 687 Å² buried · 11 hydrogen bonds · protein-protein
G–A · 655 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 disulfide (disulfide).

Compared structures

4Z14 · Recombinantly expressed latent aurone synthase (polyphenol oxidase) · the same entry in another collection · chain D against D, 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 4Z14 · PDBe 4Z14 · UniProt A0A075DN54

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