Research workbench
Crystal structure of a benzoate coenzyme a ligase with 2-thiophene carboxylic acid
Analyse Crystal structure of a benzoate coenzyme a ligase with 2-thiophene carboxylic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RMN
- Type
- protein
- Length
- 1,037 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Benzoate-coenzyme a ligase
- UniProt
- Q93TK0
- Ligands
- C21
- Pockets
- 8 · best druggability 0.80
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 | 518 | 30% helix, 26% strand | Q93TK0 |
| B | Benzoate-coenzyme a ligase | protein | 519 | 30% helix, 26% strand | Q93TK0 |
Ligands and binding sites
- C21 · Thiophene-2-carboxylic acid · ligand · 4 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 769 | 0.80 | 0.84 | 88 | C21, GOL |
| 2 | 924 | 0.80 | 0.82 | 99 | C21 |
| 3 | 598 | 0.72 | 0.80 | 53 | empty |
| 4 | 220 | 0.57 | 0.79 | 36 | empty |
| 5 | 203 | 0.55 | 0.79 | 35 | GOL |
Interfaces
1 interface between chains.
- A–B · 508 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4RMN · Crystal structure of a benzoate coenzyme A ligase with 2-Thiophene Carboxylic 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 4RMN · PDBe 4RMN · UniProt Q93TK0
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