MolNFT v1 · #126635 · protein
Crystal structure of human tyrosinase related protein 1 mutant (T391V- R374S-Y362F) in complex with kojic acid
5M8Q · 5,6-dihydroxyindole-2-carboxylic acid oxidase: “Crystal structure of human tyrosinase related protein 1 mutant (T391V- R374S-Y362F) in complex with kojic acid”. X-ray diffraction, 5 ligands (KOJ, NAG, MAN), 20 pockets (best…
- PDB
- 5M8Q
- Type
- protein
- Length
- 1,784 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5,6-dihydroxyindole-2-carboxylic acid oxidase
- EC
- 1.14.18.-
- UniProt
- P17643
- Ligands
- KOJ, NAG, MAN, FUC, ZN
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 5,6-dihydroxyindole-2-carboxylic acid oxidase (EC 1.14.18.-) | protein | 446 | 30% helix, 15% strand | P17643 |
Ligands and binding sites
- KOJ · 5-hydroxy-2-(hydroxymethyl)-4H-pyran-4-one · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 25 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 6 copies
- FUC · alpha-L-fucopyranose · sugar · 5 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 9 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 652 | 0.80 | 0.85 | 77 | empty |
| 2 | 672 | 0.80 | 0.84 | 73 | empty |
| 3 | 834 | 0.78 | 0.81 | 83 | empty |
| 4 | 792 | 0.76 | 0.80 | 70 | empty |
| 5 | 448 | 0.63 | 0.77 | 53 | NAG, FUC |
Interfaces
6 interfaces between chains.
- C–D · 547 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 358 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 329 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 311 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 216 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide, 16 glycan (disulfide, N-glycosylation).
Compared structures
- 5M8Q · Crystal structure of human tyrosinase related protein 1 mutant (T391V-R374S-Y362F) in… · the same entry in another collection · chain A against A, TM-score 1.00
- P17643 · AlphaFold monomer V2.0 prediction for 5,6-dihydroxyindole-2-carboxylic acid oxidase… · a predicted model of the same protein · 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 P17643
- Elsewhere: RCSB PDB 5M8Q · PDBe 5M8Q · UniProt P17643
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