Research workbench
4-chlorobenzoyl-CoA LIGASE/SYNTHETASE in the thioester-forming conformation, bound to 4-chlorophenacyl-CoA
Analyse 4-chlorobenzoyl-CoA LIGASE/SYNTHETASE in the thioester-forming conformation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CW9
- Type
- protein
- Length
- 1,006 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-chlorobenzoyl CoA ligase
- EC
- 6.2.1.33
- Ligands
- AMP, 01A, MG, NO3
- Pockets
- 14 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 4-chlorobenzoyl CoA ligase (EC 6.2.1.33) | protein | 503 | 32% helix, 28% strand | — |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- 01A · 4-Chlorophenacyl-coenzyme A · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- NO3 · Nitrate ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 968 | 0.82 | 0.83 | 113 | AMP, 01A, NO3 |
| 2 | 851 | 0.81 | 0.83 | 102 | AMP, 01A, NO3 |
| 3 | 82 | 0.64 | 0.90 | 19 | EDO |
| 4 | 227 | 0.54 | 0.78 | 32 | empty |
| 5 | 115 | 0.47 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1447 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 3CW9 · 4-Chlorobenzoyl-CoA Ligase/Synthetase in the Thioester-forming Conformation, bound to… · 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
- Elsewhere: RCSB PDB 3CW9 · PDBe 3CW9
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