Research workbench
In vitro and in vivo inhibition of human D-amino acid oxidase: regulation of D-serine concentration in the brain
Analyse In vitro and in vivo inhibition of human D-amino acid oxidase: regulation of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZNO
- Type
- protein
- Length
- 680 residues
- Chains
- 2
- 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, SE5
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | D-amino-acid oxidase (EC 1.4.3.3) | protein | 340 | 32% helix, 29% strand | P14920 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- SE5 · 4-(4-chlorophenethyl)-1H-pyrrole-2-carboxylic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 510 | 0.85 | 0.91 | 74 | FAD, SE5 |
| 2 | 574 | 0.85 | 0.90 | 72 | FAD, SE5 |
| 3 | 70 | 0.73 | 0.97 | 19 | GOL |
| 4 | 55 | 0.72 | 0.99 | 16 | empty |
| 5 | 188 | 0.60 | 0.82 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 1640 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3ZNO · In vitro and in vivo inhibition of human D-amino acid oxidase: regulation of D-serine… · 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 0.98
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 3ZNO · PDBe 3ZNO · UniProt P14920
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