MolNFT v1 · #126630 · protein
Crystal structure of human tyrosinase related protein 1
5M8L · 5,6-dihydroxyindole-2-carboxylic acid oxidase: “Crystal structure of human tyrosinase related protein 1”. X-ray diffraction, 4 ligands (NAG, FUC, MAN), 18 pockets (best druggability 0.78). MolNFT v1 #126630 on GenesisL1: 3D…
- PDB
- 5M8L
- 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
- NAG, FUC, MAN, ZN
- Pockets
- 18 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 11% 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, 11% strand | P17643 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 37 copies · chains A, D, B, C
- FUC · alpha-L-fucopyranose · sugar · 9 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A, C
- 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
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 956 | 0.78 | 0.81 | 83 | empty |
| 2 | 1153 | 0.77 | 0.79 | 99 | NAG |
| 3 | 764 | 0.77 | 0.81 | 68 | empty |
| 4 | 914 | 0.76 | 0.79 | 85 | NAG |
| 5 | 608 | 0.61 | 0.73 | 48 | NAG |
Interfaces
6 interfaces between chains.
- A–B · 450 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 354 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 310 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 235 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 206 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide, 22 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 5M8L · Crystal structure of human tyrosinase related protein 1 · 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 5M8L · PDBe 5M8L · UniProt P17643
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