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Crystal structure of DAAO(Y228L/R283G) variant (S-methylbenzylamine binding form)
Analyse Crystal structure of DAAO(Y228L/R283G) variant (S-methylbenzylamine binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YJF
- 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, 98B, SO4
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-amino-acid oxidase (EC 1.4.3.3) | protein | 341 | 33% helix, 29% strand | P00371 |
| B | D-amino-acid oxidase (EC 1.4.3.3) | protein | 339 | 33% helix, 29% strand | P00371 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- 98B · (1S)-1-phenylethanamine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 564 | 0.85 | 0.90 | 68 | FAD, 98B |
| 2 | 620 | 0.83 | 0.88 | 77 | FAD, 98B |
| 3 | 59 | 0.70 | 0.97 | 21 | empty |
| 4 | 60 | 0.69 | 0.96 | 20 | empty |
| 5 | 53 | 0.47 | 0.86 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1612 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4YJF · Crystal structure of DAAO(Y228L/R283G) variant (S-methylbenzylamine binding form) · 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 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 P00371
- Elsewhere: RCSB PDB 4YJF · PDBe 4YJF · UniProt P00371
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