Research workbench
Three-dimensional structure of the purple intermediate of porcine kidney D-amino acid oxidase
Analyse Three-dimensional structure of the purple intermediate of porcine kidney… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EVI
- Type
- protein
- Length
- 680 residues
- Chains
- 2
- 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, 2PC
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | D-amino acid oxidase (EC 1.4.3.3) | protein | 340 | 31% helix, 29% strand | P00371 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- 2PC · 3,4-dihydro-2H-pyrrolium-5-carboxylate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 346 | 0.85 | 0.94 | 56 | FAD, 2PC |
| 2 | 340 | 0.85 | 0.94 | 57 | FAD, 2PC |
| 3 | 58 | 0.69 | 0.97 | 21 | empty |
| 4 | 62 | 0.69 | 0.95 | 20 | empty |
| 5 | 102 | 0.43 | 0.78 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1586 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 1EVI · Three-dimensional structure of the purple intermediate of porcine kidney D-amino acid… · the same entry in another collection · chain A against A, TM-score 1.00
- P00371 · AlphaFold monomer V2.0 prediction for D-amino-acid oxidase (P00371) · 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 P00371
- Elsewhere: RCSB PDB 1EVI · PDBe 1EVI · UniProt P00371
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