MolNFT v1 · #111782 · protein
Latent aurone synthase (polyphenol oxidase) from natural source
4Z11: “Latent aurone synthase (polyphenol oxidase) from natural source”. X-ray diffraction, 1 ligand (CU), 20 pockets (best druggability 0.83). MolNFT v1 #111782 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4Z11
- Type
- protein
- Length
- 2,013 residues
- Chains
- 4
- 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 · 4 distinct chains · 27% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aurone synthase | protein | 513 | 27% helix, 19% strand | A0A075DN54 |
| B | Aurone synthase | protein | 489 | 27% helix, 20% strand | A0A075DN54 |
| C | Aurone synthase | protein | 510 | 27% helix, 19% strand | A0A075DN54 |
| D | Aurone synthase | protein | 501 | 27% helix, 20% strand | A0A075DN54 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1152 | 0.83 | 0.84 | 97 | empty |
| 2 | 1037 | 0.82 | 0.83 | 77 | empty |
| 3 | 867 | 0.76 | 0.80 | 109 | empty |
| 4 | 57 | 0.66 | 0.95 | 22 | empty |
| 5 | 50 | 0.65 | 0.96 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–B · 720 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 704 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 456 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 282 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 19 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 4Z11 · Latent aurone synthase (polyphenol oxidase) from natural source · 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 4Z11 · PDBe 4Z11 · UniProt A0A075DN54
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