MolNFT v1 · #35328 · protein
Crystal structure of human D-amino acid oxidase complexed with imino-dopa
2E82 · D-amino-acid oxidase: “Crystal structure of human D-amino acid oxidase complexed with imino-dopa”. X-ray diffraction, 2 ligands (FAD, IM3), 13 pockets (best druggability 0.86). MolNFT v1 #35328 on GenesisL1: 3D structure, binding…
- PDB
- 2E82
- 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, IM3
- Pockets
- 13 · best druggability 0.86
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
- IM3 · (2E)-3-(3,4-dihydroxyphenyl)-2-iminopropanoic 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 571 | 0.86 | 0.91 | 75 | FAD, IM3 |
| 2 | 536 | 0.86 | 0.92 | 71 | FAD, IM3 |
| 3 | 554 | 0.86 | 0.91 | 69 | FAD, IM3 |
| 4 | 626 | 0.85 | 0.90 | 80 | FAD, IM3 |
| 5 | 719 | 0.80 | 0.84 | 91 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1673 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1670 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 724 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 705 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 17 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2E82 · Crystal structure of human D-amino acid oxidase complexed with imino-DOPA · the same entry in another collection · chain C against C, 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 2E82 · PDBe 2E82 · UniProt P14920
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