Research workbench
Crystal structure of human D-amino acid oxidase in complex with O-aminobenzoate
Analyse Crystal structure of human D-amino acid oxidase in complex with O-aminobenzoate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2E4A
- 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, BE2
- Pockets
- 13 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 34% 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 | 340 | 34% helix, 29% strand | P14920 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- BE2 · 2-aminobenzoic 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
13 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1119 | 0.88 | 0.90 | 121 | FAD, BE2 |
| 2 | 1172 | 0.88 | 0.89 | 122 | FAD, BE2 |
| 3 | 777 | 0.82 | 0.85 | 87 | empty |
| 4 | 659 | 0.80 | 0.85 | 72 | empty |
| 5 | 189 | 0.65 | 0.85 | 27 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1703 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1685 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 755 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 717 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2E4A · Crystal Structure of Human D-Amino Acid Oxidase in complex with o-aminobenzoate · 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 2E4A · PDBe 2E4A · UniProt P14920
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