MolNFT v1 · #175518 · protein
Crystal structure of D-amino acid oxidase from rasamsonia emersonii strain ya
7CT4: “Crystal structure of D-amino acid oxidase from rasamsonia emersonii strain ya”. X-ray diffraction, 1 ligand (FAD), 18 pockets (best druggability 0.86). MolNFT v1 #175518 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7CT4
- Type
- protein
- Length
- 1,376 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-amino acid oxidase
- UniProt
- A0A499UB99
- Ligands
- FAD
- Pockets
- 18 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-amino acid oxidase | protein | 341 | 29% helix, 30% strand | A0A499UB99 |
| B | D-amino acid oxidase | protein | 346 | 29% helix, 30% strand | A0A499UB99 |
| C | D-amino acid oxidase | protein | 347 | 30% helix, 30% strand | A0A499UB99 |
| D | D-amino acid oxidase | protein | 342 | 30% helix, 32% strand | A0A499UB99 |
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
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 917 | 0.86 | 0.88 | 125 | FAD |
| 2 | 553 | 0.85 | 0.90 | 76 | FAD |
| 3 | 584 | 0.85 | 0.90 | 80 | FAD |
| 4 | 447 | 0.83 | 0.91 | 62 | FAD |
| 5 | 54 | 0.71 | 0.98 | 18 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1262 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1246 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 556 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 548 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 255 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7CT4 · Crystal structure of D-amino acid oxidase from Rasamsonia emersonii strain YA · the same entry in another collection · chain C against C, TM-score 1.00
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 A0A499UB99
- Elsewhere: RCSB PDB 7CT4 · PDBe 7CT4 · UniProt A0A499UB99
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