MolNFT v1 · #150192 · protein
Structure of human hydroxyacid oxidase 1 bound with FMN and glycolate
6GMB: “Structure of human hydroxyacid oxidase 1 bound with FMN and glycolate”. X-ray diffraction, 2 ligands (FMN, GOA), 4 pockets (best druggability 0.81). MolNFT v1 #150192 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6GMB
- Type
- protein
- Length
- 362 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydroxyacid oxidase 1
- EC
- 1.1.3.15
- UniProt
- Q9UJM8
- Ligands
- FMN, GOA
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hydroxyacid oxidase 1 (EC 1.1.3.15) | protein | 362 | 45% helix, 14% strand | Q9UJM8 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · chains A
- GOA · Glycolic acid · ligand · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 150 | 0.81 | 0.98 | 32 | FMN, GOA |
| 2 | 131 | 0.46 | 0.77 | 25 | empty |
| 3 | 59 | 0.32 | 0.76 | 21 | EDO, PG4 |
| 4 | 65 | 0.28 | 0.73 | 14 | empty |
Compared structures
- 6GMB · Structure of human hydroxyacid oxidase 1 bound with FMN and glycolate · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UJM8 · AlphaFold monomer V2.0 prediction for hydroxyacid oxidase 1 (Q9UJM8) · a predicted model of the same protein · chain A 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 6GMB · PDBe 6GMB · UniProt Q9UJM8
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