MolNFT v1 · #172219 · protein
Psychrophilic aromatic amino acids aminotransferase from psychrobacter sp. B6 cocrystalized with substrate analog - L-indole-3-lactic acid
6ZVG: “Psychrophilic aromatic amino acids aminotransferase from psychrobacter sp. B6 cocrystalized with substrate…”. X-ray diffraction, 4 ligands (PLP, 3IL, MG), 16 pockets (best druggability 0.84). MolNFT v1 #172219 on GenesisL1: 3D…
- PDB
- 6ZVG
- Type
- protein
- Length
- 1,572 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminotransferase
- EC
- 2.6.1.-
- UniProt
- C7E5X4
- Ligands
- PLP, 3IL, MG, NO3
- Pockets
- 16 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Aminotransferase (EC 2.6.1.-) | protein | 398 | 48% helix, 14% strand | C7E5X4 |
| B, D | Aminotransferase (EC 2.6.1.-) | protein | 388 | 49% helix, 13% strand | C7E5X4 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- 3IL · 3-(indol-3-yl) lactate · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 3 copies · chains A, B, C, D
- NO3 · Nitrate ion · ion · 2 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 740 | 0.84 | 0.87 | 121 | MG, NO3 |
| 2 | 140 | 0.80 | 0.97 | 35 | PLP, 3IL |
| 3 | 200 | 0.76 | 0.91 | 42 | PLP, 3IL |
| 4 | 273 | 0.75 | 0.88 | 44 | PLP |
| 5 | 186 | 0.68 | 0.87 | 27 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2799 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 2749 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 598 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 512 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 481 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6ZVG · Psychrophilic aromatic amino acids aminotransferase from Psychrobacter sp. B6… · 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 C7E5X4
- Elsewhere: RCSB PDB 6ZVG · PDBe 6ZVG · UniProt C7E5X4
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