Research workbench
Crystallographic structure of D-amino acid aminotransferase in pyridoxal-5'-phosphate (plp) form
Analyse Crystallographic structure of D-amino acid aminotransferase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DAA
- Type
- protein
- Length
- 554 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-amino acid aminotransferase
- EC
- 2.6.1.21
- UniProt
- P19938
- Ligands
- PLP, SO4
- Pockets
- 3 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | D-amino acid aminotransferase (EC 2.6.1.21) | protein | 277 | 30% helix, 31% strand | P19938 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 957 | 0.83 | 0.84 | 115 | SO4, PLP |
| 2 | 81 | 0.40 | 0.78 | 13 | empty |
| 3 | 61 | 0.37 | 0.79 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 2278 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 4DAA · Crystallographic structure of D-amino acid aminotransferase in pyridoxal-5'-phosphate… · the same entry in another collection · chain A against A, TM-score 1.00
- P19938 · AlphaFold monomer V2.0 prediction for D-alanine aminotransferase (P19938) · a predicted model of the same protein · chain B 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 P19938
- Elsewhere: RCSB PDB 4DAA · PDBe 4DAA · UniProt P19938
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