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The crystal structure of benzoate coenzyme A ligase double mutant (H333A/I334A) in complex with 2-methyl-thiazole-5 carboxylate-AMP
Analyse The crystal structure of benzoate coenzyme A ligase double mutant (H333A/I334A)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M2T
- Type
- protein
- Length
- 2,072 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.14
- Source
- Rhodopseudomonas palustris
- Molecule
- Benzoate-coenzyme A ligase
- UniProt
- Q93TK0
- Ligands
- AMP, 6V9
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.14 · 1 distinct chain · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Benzoate-coenzyme A ligase | protein | 518 | 30% helix, 25% strand | Q93TK0 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 4 copies · chains A, B, C, D
- 6V9 · 2-methyl-1,3-thiazole-5-carboxylic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1064 | 0.82 | 0.83 | 120 | AMP, 6V9 |
| 2 | 968 | 0.82 | 0.83 | 106 | AMP, 6V9 |
| 3 | 1010 | 0.81 | 0.82 | 111 | AMP, 6V9 |
| 4 | 1167 | 0.81 | 0.82 | 116 | AMP, 6V9 |
| 5 | 608 | 0.71 | 0.79 | 55 | empty |
Interfaces
4 interfaces between chains.
- B–D · 463 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 252 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 195 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 134 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6M2T · The crystal structure of benzoate coenzyme a ligase double mutant (H333A/I334A) in… · 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 6M2T · PDBe 6M2T · UniProt Q93TK0
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