MolNFT v1 · #8362 · protein
Involvement of TYR24 and TRP108 in substrate binding and substrate specificity of glycolate oxidase
1GYL: “Involvement of TYR24 and TRP108 in substrate binding and substrate specificity of glycolate oxidase”. X-ray diffraction, 1 ligand (FMN), 8 pockets (best druggability 0.79). MolNFT v1 #8362 on GenesisL1: 3D structure, binding sites…
- 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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