MolNFT v1 · #149572 · protein
Crystal structure of the omega transaminase from pseudomonas jessenii in complex with pmp
6G4F · Aspartate aminotransferase family protein: “Crystal structure of the omega transaminase from pseudomonas jessenii in complex with pmp”. X-ray diffraction, 2 ligands (PMP, PLP), 8 pockets (best druggability 0.77). MolNFT v1 #149572…
- PDB
- 6G4F
- Type
- protein
- Length
- 904 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate aminotransferase family protein
- UniProt
- A0A2D8IND4
- Ligands
- PMP, PLP
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aspartate aminotransferase family protein | protein | 451 | 44% helix, 17% strand | A0A2D8IND4 |
| B | Aspartate aminotransferase family protein | protein | 453 | 43% helix, 17% strand | A0A2D8IND4 |
Ligands and binding sites
- PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · chains A, B
- PLP · Pyridoxal-5'-phosphate · ligand · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 894 | 0.77 | 0.80 | 88 | PMP |
| 2 | 776 | 0.75 | 0.80 | 83 | PLP |
| 3 | 97 | 0.39 | 0.76 | 19 | empty |
| 4 | 82 | 0.36 | 0.76 | 19 | empty |
| 5 | 90 | 0.35 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 5437 Ų buried · 93 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6G4F · Crystal structure of the omega TRANSAMINASE FROM PSEUDOMONAS Jessenii in complex with PMP · 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 A0A2D8IND4
- Elsewhere: RCSB PDB 6G4F · PDBe 6G4F · UniProt A0A2D8IND4
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