Research workbench
Crystal structure of GenB3 in complex with PLP
Analyse Crystal structure of GenB3 in complex with PLP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LM0
- Type
- protein
- Length
- 895 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.09
- Source
- Micromonospora echinospora
- Molecule
- C-6' aminotransferase
- UniProt
- Q70KE4
- Ligands
- PLP
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.09 · 2 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C-6' aminotransferase | protein | 449 | 44% helix, 14% strand | Q70KE4 |
| B | C-6' aminotransferase | protein | 446 | 45% helix, 14% strand | Q70KE4 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 177 | 0.82 | 0.97 | 27 | empty |
| 2 | 688 | 0.76 | 0.81 | 65 | PLP |
| 3 | 685 | 0.75 | 0.81 | 71 | PLP |
| 4 | 103 | 0.47 | 0.80 | 18 | empty |
| 5 | 84 | 0.37 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 4425 Ų buried · 76 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 7LM0 · Crystal structure of GENB3 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 Q70KE4
- Elsewhere: RCSB PDB 7LM0 · PDBe 7LM0 · UniProt Q70KE4
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