Research workbench
Crystal structure of pige: a transaminase involved in the biosynthesis of 2-methyl-3-N-amyl-pyrrole (MAP) from serratia sp. FS14
Analyse Crystal structure of pige: a transaminase involved in the biosynthesis of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PPM
- Type
- protein
- Length
- 926 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminotransferase
- UniProt
- A0A059ZJX2
- Ligands
- PLP, MG
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminotransferase | protein | 464 | 46% helix, 16% strand | A0A059ZJX2 |
| B | Aminotransferase | protein | 462 | 47% helix, 15% strand | A0A059ZJX2 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 634 | 0.80 | 0.85 | 78 | PLP |
| 2 | 571 | 0.80 | 0.86 | 82 | PLP |
| 3 | 83 | 0.77 | 0.98 | 26 | empty |
| 4 | 74 | 0.76 | 0.98 | 25 | empty |
| 5 | 144 | 0.42 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 5948 Ų buried · 63 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 4PPM · Crystal structure of PigE: a transaminase involved in the biosynthesis of… · 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 A0A059ZJX2
- Elsewhere: RCSB PDB 4PPM · PDBe 4PPM · UniProt A0A059ZJX2
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