Research workbench
Crystal structure of human D-amino acid oxidase: bound to an inhibitor
Analyse Crystal structure of human D-amino acid oxidase: bound to an inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CUK
- Type
- protein
- Length
- 1,308 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, 4P5
- Pockets
- 8 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | D-amino-acid oxidase (EC 1.4.3.3) | protein | 327 | 35% helix, 29% strand | P14920 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- 4P5 · 4H-furo[3,2-b]pyrrole-5-carboxylic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1140 | 0.88 | 0.90 | 145 | FAD, 4P5 |
| 2 | 1173 | 0.88 | 0.89 | 143 | FAD, 4P5 |
| 3 | 976 | 0.82 | 0.84 | 94 | empty |
| 4 | 1172 | 0.80 | 0.81 | 96 | empty |
| 5 | 78 | 0.38 | 0.77 | 17 | empty |
Interfaces
2 interfaces between chains.
- B–D · 735 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 711 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3CUK · Crystal structure of human D-amino acid oxidase: bound to an 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 3CUK · PDBe 3CUK · UniProt P14920
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