Research workbench
Crystal structure of PPO3, a tyrosinase from agaricus bisporus, in deoxy-form that contains additional unknown lectin-like subunit, with inhibitor tropolone
Analyse Crystal structure of PPO3, a tyrosinase from agaricus bisporus, in deoxy-form… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y9X
- Type
- protein
- Length
- 2,108 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyphenol oxidase; Lectin-like fold protein
- EC
- 1.14.18.1
- UniProt
- C7FF04
- Ligands
- 0TR, CU, HO
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Polyphenol oxidase (EC 1.14.18.1) | protein | 391 | 42% helix, 9% strand | C7FF04 |
| E, F, G, H | Lectin-like fold protein | protein | 136 | 5% helix, 47% strand | — |
Ligands and binding sites
- 0TR · 2-hydroxycyclohepta-2,4,6-trien-1-one · ligand · 4 copies · chains A, B, C, D
- CU · Copper (II) ion · metal · 8 copies · chains A, B, C, D
- HO · Holmium atom · metal · 4 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1048 | 0.83 | 0.84 | 123 | empty |
| 2 | 1009 | 0.79 | 0.81 | 68 | HO |
| 3 | 429 | 0.79 | 0.87 | 59 | empty |
| 4 | 441 | 0.79 | 0.87 | 62 | empty |
| 5 | 987 | 0.78 | 0.80 | 68 | empty |
Interfaces
19 interfaces between chains.
- D–H · 841 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 831 Ų buried · 6 hydrogen bonds · protein-protein
- C–G · 813 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 802 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 715 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 2Y9X · Crystal structure of PPO3, a tyrosinase from Agaricus bisporus, in deoxy-form that… · the same entry in another collection · chain H against H, TM-score 1.00
- C7FF04 · AlphaFold monomer V2.0 prediction for polyphenol oxidase 3 (C7FF04) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 C7FF04
- Elsewhere: RCSB PDB 2Y9X · PDBe 2Y9X · UniProt C7FF04
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