MolNFT v1 · #147917 · protein
Crystal structure of diaminopelargonic acid aminotransferase from psychrobacter cryohalolentis
6ERK: “Crystal structure of diaminopelargonic acid aminotransferase from psychrobacter cryohalolentis”. X-ray diffraction, 2 ligands (PLP, SO4), 4 pockets (best druggability 0.75). MolNFT v1 #147917 on GenesisL1: 3D structure, binding…
- PDB
- 6ERK
- Type
- protein
- Length
- 838 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminotransferase
- EC
- 2.6.1.-
- UniProt
- Q1QDV8
- Ligands
- PLP, SO4
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminotransferase (EC 2.6.1.-) | protein | 420 | 41% helix, 19% strand | Q1QDV8 |
| B | Aminotransferase (EC 2.6.1.-) | protein | 418 | 40% helix, 19% strand | Q1QDV8 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 498 | 0.75 | 0.83 | 73 | PLP |
| 2 | 642 | 0.74 | 0.81 | 80 | PLP |
| 3 | 76 | 0.34 | 0.76 | 17 | empty |
| 4 | 67 | 0.31 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 4265 Ų buried · 60 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6ERK · Crystal structure of diaminopelargonic acid aminotransferase from Psychrobacter… · 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 Q1QDV8
- Elsewhere: RCSB PDB 6ERK · PDBe 6ERK · UniProt Q1QDV8
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