MolNFT v1 · #191198 · protein
Crystal structure of D-amino acid aminotransferase from aminobacterium colombiense in holo form with plp
8AHR · Aminotransferase class IV: “Crystal structure of D-amino acid aminotransferase from aminobacterium colombiense in holo form with plp”. X-ray diffraction, 1 ligand (PLP), 2 pockets (best druggability 0.81). MolNFT v1 #191198 on…
- PDB
- 8AHR
- Type
- protein
- Length
- 542 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminotransferase class IV
- UniProt
- D5EHC5
- Ligands
- PLP
- Pockets
- 2 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aminotransferase class IV | protein | 271 | 31% helix, 31% strand | D5EHC5 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 790 | 0.81 | 0.84 | 74 | PLP |
| 2 | 466 | 0.68 | 0.80 | 48 | PLP |
Interfaces
1 interface between chains.
- A–B · 1869 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 8AHR · Crystal structure of D-amino acid aminotransferase from Aminobacterium colombiense in… · the same entry in another collection · 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 D5EHC5
- Elsewhere: RCSB PDB 8AHR · PDBe 8AHR · UniProt D5EHC5
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