Research workbench
Crystal structure of tyrosinase from bacillus megaterium with inhibitor kojic acid in the active site
Analyse Crystal structure of tyrosinase from bacillus megaterium with inhibitor kojic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I38
- Type
- protein
- Length
- 573 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosinase
- UniProt
- B2ZB02
- Ligands
- KOJ, CU
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosinase | protein | 286 | 42% helix, 5% strand | B2ZB02 |
| B | Tyrosinase | protein | 287 | 41% helix, 5% strand | B2ZB02 |
Ligands and binding sites
- KOJ · 5-hydroxy-2-(hydroxymethyl)-4H-pyran-4-one · ligand · 2 copies · chains A, B
- CU · Copper (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 519 | 0.74 | 0.82 | 90 | KOJ |
| 2 | 56 | 0.36 | 0.79 | 16 | empty |
| 3 | 61 | 0.35 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1182 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5I38 · Crystal Structure of tyrosinase from Bacillus megaterium with inhibitor kojic acid in the… · 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 B2ZB02
- Elsewhere: RCSB PDB 5I38 · PDBe 5I38 · UniProt B2ZB02
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