Research workbench
Crystal structure of a benzoate coenzyme A ligase with o-Toluic acid
Analyse Crystal structure of a benzoate coenzyme A ligase with o-Toluic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RLQ
- Type
- protein
- Length
- 1,037 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.63
- Source
- Rhodopseudomonas palustris
- Molecule
- Benzoate-coenzyme A ligase
- UniProt
- Q93TK0
- Ligands
- 3SK
- Pockets
- 7 · best druggability 0.90
Structure
x-ray diffraction · resolution 1.63 · 2 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Benzoate-coenzyme A ligase | protein | 518 | 30% helix, 26% strand | Q93TK0 |
| B | Benzoate-coenzyme A ligase | protein | 519 | 30% helix, 26% strand | Q93TK0 |
Ligands and binding sites
- 3SK · 2-methylbenzoic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.90 | 0.91 | 170 | 3SK, GOL |
| 2 | 178 | 0.65 | 0.85 | 38 | empty |
| 3 | 333 | 0.64 | 0.80 | 36 | empty |
| 4 | 217 | 0.56 | 0.79 | 33 | GOL |
| 5 | 117 | 0.47 | 0.79 | 27 | GOL |
Interfaces
1 interface between chains.
- A–B · 1498 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4RLQ · Crystal structure of a benzoate coenzyme a ligase with O-toluic acid · 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 Q93TK0
- Elsewhere: RCSB PDB 4RLQ · PDBe 4RLQ · UniProt Q93TK0
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