Research workbench
Crystal structure of human D-amino acid oxidase in complex with inhibitor
Analyse Crystal structure of human D-amino acid oxidase in complex with inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7U9U
- Type
- protein
- Length
- 679 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.66
- Source
- Homo sapiens
- Molecule
- D-amino-acid oxidase
- EC
- 1.4.3.3
- UniProt
- P14920
- Ligands
- FAD, BEZ, M89
- Pockets
- 9 · best druggability 0.88
Structure
x-ray diffraction · resolution 1.66 · 2 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-amino-acid oxidase (EC 1.4.3.3) | protein | 340 | 35% helix, 29% strand | P14920 |
| B | D-amino-acid oxidase (EC 1.4.3.3) | protein | 339 | 33% helix, 29% strand | P14920 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- BEZ · Benzoic acid · ligand · chains A
- M89 · (3R)-3-(5,6-dioxo-1,4,5,6-tetrahydropyrazin-2-yl)-2,3-dihydro-1,4-benzoxathiine-7-carbonitrile · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1154 | 0.88 | 0.89 | 133 | FAD, BEZ, M89 |
| 2 | 1179 | 0.80 | 0.82 | 92 | empty |
| 3 | 136 | 0.59 | 0.84 | 19 | empty |
| 4 | 70 | 0.51 | 0.85 | 19 | empty |
| 5 | 96 | 0.51 | 0.82 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 818 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7U9U · Crystal structure of human D-amino acid oxidase in complex with inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P14920 · AlphaFold monomer V2.0 prediction for D-amino-acid oxidase (P14920) · 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 P14920
- Elsewhere: RCSB PDB 7U9U · PDBe 7U9U · UniProt P14920
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.