MolNFT v1 · #149570 · protein
Crystal structure of the omega transaminase from pseudomonas jessenii in complex with plp
6G4D · Aspartate aminotransferase family protein: “Crystal structure of the omega transaminase from pseudomonas jessenii in complex with plp”. X-ray diffraction, 1 ligand (PLP), 6 pockets (best druggability 0.77). MolNFT v1 #149570 on…
- PDB
- 6G4D
- 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
- PLP
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aspartate aminotransferase family protein | protein | 451 | 43% helix, 17% strand | A0A2D8IND4 |
| B | Aspartate aminotransferase family protein | protein | 453 | 43% helix, 17% strand | A0A2D8IND4 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 864 | 0.77 | 0.80 | 91 | PLP, GOL |
| 2 | 773 | 0.76 | 0.80 | 82 | PLP |
| 3 | 84 | 0.35 | 0.75 | 19 | empty |
| 4 | 84 | 0.33 | 0.74 | 18 | empty |
| 5 | 56 | 0.29 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 5499 Ų buried · 89 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6G4D · Crystal structure of the omega TRANSAMINASE FROM PSEUDOMONAS Jessenii in complex with PLP · 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 6G4D · PDBe 6G4D · UniProt A0A2D8IND4
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