Research workbench
Crystal structure of human glycolate oxidase in complex with the inhibitor 5-[(4-CHLOROPHENYL)SULFANYL]- 1,2,3-thiadiazole-4- carboxylate.
Analyse Crystal structure of human glycolate oxidase in complex with the inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2W0U
- Type
- protein
- Length
- 1,333 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydroxyacid oxidase 1
- EC
- 1.1.3.15
- UniProt
- Q9UJM8
- Ligands
- C7C, FMN
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hydroxyacid oxidase 1 (EC 1.1.3.15) | protein | 334 | 48% helix, 16% strand | Q9UJM8 |
| B | Hydroxyacid oxidase 1 (EC 1.1.3.15) | protein | 333 | 48% helix, 15% strand | Q9UJM8 |
| C | Hydroxyacid oxidase 1 (EC 1.1.3.15) | protein | 332 | 48% helix, 16% strand | Q9UJM8 |
| D | Hydroxyacid oxidase 1 (EC 1.1.3.15) | protein | 334 | 47% helix, 15% strand | Q9UJM8 |
Ligands and binding sites
- C7C · 5-[(4-chlorophenyl)sulfanyl]-1,2,3-thiadiazole-4-carboxylate · ligand · 4 copies · chains A, B, C, D
- FMN · Flavin mononucleotide · ligand · 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 302 | 0.80 | 0.91 | 43 | C7C, FMN |
| 2 | 272 | 0.79 | 0.91 | 44 | C7C, FMN |
| 3 | 273 | 0.79 | 0.91 | 43 | C7C, FMN |
| 4 | 329 | 0.78 | 0.88 | 52 | C7C, FMN |
| 5 | 650 | 0.72 | 0.79 | 53 | empty |
Interfaces
3 interfaces between chains.
- B–C · 467 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 181 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 162 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2W0U · Crystal structure of human glycolate oxidase in complex with the inhibitor… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9UJM8 · AlphaFold monomer V2.0 prediction for hydroxyacid oxidase 1 (Q9UJM8) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q9UJM8
- Elsewhere: RCSB PDB 2W0U · PDBe 2W0U · UniProt Q9UJM8
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