Research workbench
Pandda analysis group deposition of models with modelled events (E.G. bound ligands) -- crystal structure of HAO1 in complex with Z30620520
Analyse Pandda analysis group deposition of models with modelled events (E.G. bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5QIC
- Type
- protein
- Length
- 344 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, GX4
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hydroxyacid oxidase 1 (EC 1.1.3.15) | protein | 344 | 47% helix, 15% strand | Q9UJM8 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · chains A
- GX4 · cyclopropyl-[4-(4-fluorophenyl)piperazin-1-yl]methanone · ligand · 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 | 164 | 0.82 | 0.97 | 31 | FMN |
| 2 | 137 | 0.48 | 0.78 | 25 | empty |
| 3 | 53 | 0.31 | 0.76 | 12 | empty |
| 4 | 53 | 0.26 | 0.73 | 16 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5QIC · PanDDA analysis group deposition of models with modelled events (e.g. bound ligands)… · 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 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 Q9UJM8
- Elsewhere: RCSB PDB 5QIC · PDBe 5QIC · UniProt Q9UJM8
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