Research workbench
Crystal structure of the omega transaminase from pseudomonas jessenii in complex with pmp
Analyse Crystal structure of the omega transaminase from pseudomonas jessenii in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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