Research workbench
Crystal structure of a benzoate coenzyme a ligase with P-toluic acid and O-toluic acid
Analyse Crystal structure of a benzoate coenzyme a ligase with P-toluic acid and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RLF
- Type
- protein
- Length
- 1,035 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Benzoate-coenzyme a ligase
- UniProt
- Q93TK0
- Ligands
- 3SK, 4MA
- Pockets
- 7 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Benzoate-coenzyme a ligase | protein | 516 | 30% helix, 26% strand | Q93TK0 |
| B | Benzoate-coenzyme a ligase | protein | 519 | 29% helix, 26% strand | Q93TK0 |
Ligands and binding sites
- 3SK · 2-methylbenzoic acid · ligand · 2 copies · chains A, B
- 4MA · 4-methylbenzoic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 8 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 | 1142 | 0.89 | 0.91 | 170 | 3SK, 4MA, GOL |
| 2 | 304 | 0.63 | 0.80 | 38 | empty |
| 3 | 274 | 0.62 | 0.80 | 38 | empty |
| 4 | 156 | 0.52 | 0.80 | 19 | empty |
| 5 | 203 | 0.48 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1494 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 4RLF · Crystal structure of a benzoate coenzyme A ligase with p-Toluic acid and 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 4RLF · PDBe 4RLF · UniProt Q93TK0
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