Research workbench
Involvement of TYR24 and TRP108 in substrate binding and substrate specificity of glycolate oxidase
Analyse Involvement of TYR24 and TRP108 in substrate binding and substrate specificity… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GYL
- Type
- protein
- Length
- 702 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycolate oxidase
- EC
- 1.1.3.15
- UniProt
- P05414
- Ligands
- FMN
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycolate oxidase (EC 1.1.3.15) | protein | 352 | 33% helix, 6% strand | P05414 |
| B | Glycolate oxidase (EC 1.1.3.15) | protein | 350 | 24% helix, 5% strand | P05414 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 704 | 0.79 | 0.84 | 84 | empty |
| 2 | 470 | 0.76 | 0.84 | 61 | FMN |
| 3 | 208 | 0.57 | 0.80 | 32 | empty |
| 4 | 172 | 0.55 | 0.80 | 38 | empty |
| 5 | 123 | 0.54 | 0.82 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1420 Ų buried · 54 hydrogen bonds · protein-protein
Compared structures
- 1GYL · Involvement of TYR24 and TRP108 in substrate binding and substrate specificity of… · the same entry in another collection · chain A against A, TM-score 1.00
- P05414 · AlphaFold monomer V2.0 prediction for peroxisomal (S)-2-hydroxy-acid oxidase (P05414) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P05414
- Elsewhere: RCSB PDB 1GYL · PDBe 1GYL · UniProt P05414
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