MolNFT v1 · #103118 · protein
Crystal structure of tyrosinase from bacillus megaterium with L-dopa in the active site
4P6S: “Crystal structure of tyrosinase from bacillus megaterium with L-dopa in the active site”. X-ray diffraction, 2 ligands (DAH, ZN), 6 pockets (best druggability 0.69). MolNFT v1 #103118 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4P6S
- Type
- protein
- Length
- 573 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosinase
- EC
- 1.14.18.1
- UniProt
- B2ZB02
- Ligands
- DAH, ZN
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosinase (EC 1.14.18.1) | protein | 286 | 41% helix, 5% strand | B2ZB02 |
| B | Tyrosinase (EC 1.14.18.1) | protein | 287 | 44% helix, 6% strand | B2ZB02 |
Ligands and binding sites
- DAH · 3,4-dihydroxyphenylalanine · ligand · 4 copies · chains A, B
- ZN · Zinc ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.69 | 0.89 | 30 | empty |
| 2 | 181 | 0.61 | 0.83 | 32 | empty |
| 3 | 84 | 0.46 | 0.81 | 22 | ZN, DAH |
| 4 | 72 | 0.40 | 0.79 | 18 | DAH |
| 5 | 67 | 0.29 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1137 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4P6S · Crystal Structure of tyrosinase from Bacillus megaterium with L-DOPA in the active site · the same entry in another collection · chain B against B, 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 B2ZB02
- Elsewhere: RCSB PDB 4P6S · PDBe 4P6S · UniProt B2ZB02
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