Research workbench
Crystal structure of human D-amino acid oxidase: substrate- free holoenzyme
Analyse Crystal structure of human D-amino acid oxidase: substrate- free holoenzyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2E48
- 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
- Pockets
- 11 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 32% 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 | 32% helix, 28% strand | P14920 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1162 | 0.89 | 0.91 | 146 | FAD |
| 2 | 1159 | 0.89 | 0.91 | 146 | FAD |
| 3 | 1003 | 0.81 | 0.82 | 91 | empty |
| 4 | 787 | 0.79 | 0.83 | 82 | empty |
| 5 | 161 | 0.59 | 0.83 | 27 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1657 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1623 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 729 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 699 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2E48 · Crystal Structure of Human D-Amino Acid Oxidase: Substrate-Free Holoenzyme · 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 2E48 · PDBe 2E48 · UniProt P14920
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