MolNFT v1 · #138861 · protein
Crystal structure of porcine kidney D-amino acid oxidase mutant (I230A/R283G)
5WWV · D-amino-acid oxidase: “Crystal structure of porcine kidney D-amino acid oxidase mutant (I230A/R283G)”. X-ray diffraction, 3 ligands (FAD, 7V3, SO4), 20 pockets (best druggability 0.87). MolNFT v1 #138861 on GenesisL1: 3D structure…
- PDB
- 5WWV
- Type
- protein
- Length
- 2,707 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-amino-acid oxidase
- EC
- 1.4.3.3
- UniProt
- P00371
- Ligands
- FAD, 7V3, SO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | D-amino-acid oxidase (EC 1.4.3.3) | protein | 339 | 31% helix, 30% strand | P00371 |
| E, F, G | D-amino-acid oxidase (EC 1.4.3.3) | protein | 338 | 33% helix, 31% strand | P00371 |
| H | D-amino-acid oxidase (EC 1.4.3.3) | protein | 337 | 32% helix, 28% strand | P00371 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- 7V3 · (S)-(4-chlorophenyl)-phenyl-methanamine · ligand · 5 copies · chains A, C, D, F, G
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D, E, F, H
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 21 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 473 | 0.87 | 0.93 | 61 | FAD, 7V3 |
| 2 | 482 | 0.86 | 0.93 | 58 | FAD, MPD |
| 3 | 479 | 0.86 | 0.93 | 58 | FAD, 7V3 |
| 4 | 453 | 0.86 | 0.93 | 58 | FAD, 7V3 |
| 5 | 496 | 0.85 | 0.92 | 60 | FAD, 7V3, MPD |
Interfaces
9 interfaces between chains.
- C–D · 1621 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 1618 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1562 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1555 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 587 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5WWV · Crystal structure of porcine kidney D-amino acid oxidase mutant (I230A/R283G) · the same entry in another collection · chain H against H, TM-score 1.00
- P00371 · AlphaFold monomer V2.0 prediction for D-amino-acid oxidase (P00371) · a predicted model of the same protein · chain E 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 P00371
- Elsewhere: RCSB PDB 5WWV · PDBe 5WWV · UniProt P00371
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