Research workbench
Crystal structure of plp-bound putative aminotransferase from clostridium difficile 630 crystallized with magnesium formate
Analyse Crystal structure of plp-bound putative aminotransferase from clostridium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DGT
- Type
- protein
- Length
- 774 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative pyridoxal phosphate-dependent transferase
- UniProt
- Q183G9
- Ligands
- PLP, MG, CL
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative pyridoxal phosphate-dependent transferase | protein | 387 | 47% helix, 16% strand | Q183G9 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 9 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 893 | 0.81 | 0.83 | 90 | PLP |
| 2 | 108 | 0.40 | 0.76 | 25 | empty |
| 3 | 87 | 0.37 | 0.76 | 20 | empty |
| 4 | 82 | 0.36 | 0.76 | 14 | empty |
| 5 | 70 | 0.36 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2647 Ų buried · 46 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 4DGT · Crystal structure of PLP-bound putative aminotransferase from Clostridium difficile 630… · 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 Q183G9
- Elsewhere: RCSB PDB 4DGT · PDBe 4DGT · UniProt Q183G9
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