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Crystal structure of D-amino acid aminotrensferase from Aminobacterium colombiense complexed with D-glutamate
Analyse Crystal structure of D-amino acid aminotrensferase from Aminobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8AYK
- Type
- protein
- Length
- 551 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Aminobacterium colombiense
- Molecule
- Aminotransferase class IV
- UniProt
- D5EHC5
- Ligands
- PW0, PMP
- Pockets
- 3 · best druggability 0.84
Structure
x-ray diffraction · resolution 1.9 · 2 distinct chains · 31% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminotransferase class IV | protein | 276 | 31% helix, 30% strand | D5EHC5 |
| B | Aminotransferase class IV | protein | 275 | 31% helix, 30% strand | D5EHC5 |
Ligands and binding sites
- PW0 · (~{Z})-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]pent-2-enedioic acid · ligand · 2 copies · chains A, B
- PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 284 | 0.84 | 0.95 | 30 | empty |
| 2 | 585 | 0.72 | 0.80 | 49 | PW0, PMP |
| 3 | 548 | 0.71 | 0.80 | 47 | PW0, PMP |
Interfaces
1 interface between chains.
- A–B · 2090 Ų buried · 27 hydrogen bonds · protein-protein
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 D5EHC5
- Elsewhere: RCSB PDB 8AYK · PDBe 8AYK · UniProt D5EHC5
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