Research workbench
Crystal structure of human D-amino acid oxidase in complex with hydroxyquinolin-2(1H)
Analyse Crystal structure of human D-amino acid oxidase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3G3E
- Type
- protein
- Length
- 1,360 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-amino-acid oxidase
- EC
- 1.4.3.3
- UniProt
- P14920
- Ligands
- FAD, G3E
- Pockets
- 12 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | D-amino-acid oxidase (EC 1.4.3.3) | protein | 340 | 33% helix, 28% strand | P14920 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- G3E · 3-hydroxyquinolin-2(1H)-one · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1115 | 0.89 | 0.91 | 142 | FAD, G3E |
| 2 | 1173 | 0.89 | 0.90 | 143 | FAD, G3E |
| 3 | 849 | 0.83 | 0.85 | 113 | empty |
| 4 | 757 | 0.82 | 0.85 | 84 | empty |
| 5 | 55 | 0.56 | 0.89 | 15 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1712 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1693 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 743 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 742 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 106 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3G3E · Crystal structure of human D-amino acid oxidase in complex with hydroxyquinolin-2(1H) · 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 3G3E · PDBe 3G3E · UniProt P14920
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