Research workbench
Structure of citryl-CoA synthetase from hydrogenobacter thermophilus
Analyse Structure of citryl-CoA synthetase from hydrogenobacter thermophilus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HXQ
- Type
- protein
- Length
- 1,504 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Citryl-CoA synthetase small subunit; Citryl-CoA synthetase large subunit
- UniProt
- Q75VW6, Q75VW8
- Ligands
- COA
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Citryl-CoA synthetase small subunit | protein | 342 | 33% helix, 19% strand | Q75VW6 |
| B, D | Citryl-CoA synthetase large subunit | protein | 410 | 36% helix, 26% strand | Q75VW8 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 2 copies · chains A, D, B, C
- PGE · Triethylene glycol · additive · 4 copies · chains A, B, D, C
- FLC · Citrate anion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 945 | 0.81 | 0.83 | 60 | PGE |
| 2 | 682 | 0.77 | 0.83 | 90 | empty |
| 3 | 284 | 0.69 | 0.84 | 43 | empty |
| 4 | 379 | 0.68 | 0.81 | 54 | FLC |
| 5 | 393 | 0.66 | 0.79 | 55 | empty |
Interfaces
5 interfaces between chains.
- C–D · 3358 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 2707 Ų buried · 40 hydrogen bonds · protein-protein
- B–C · 667 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 658 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 64 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6HXQ · Structure of citryl-CoA synthetase from Hydrogenobacter thermophilus · 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 Q75VW6
- Every structure of UniProt Q75VW8
- Elsewhere: RCSB PDB 6HXQ · PDBe 6HXQ · UniProt Q75VW6 · UniProt Q75VW8
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