Research workbench
Crystal structure of citrate synthase from thermus thermophilus HB8
Analyse Crystal structure of citrate synthase from thermus thermophilus HB8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IXE
- Type
- protein
- Length
- 1,473 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Citrate synthase
- EC
- 4.1.3.7
- UniProt
- Q9LCX9
- Ligands
- COA, SO4
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 60% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Citrate synthase (EC 4.1.3.7) | protein | 371 | 61% helix, 6% strand | Q9LCX9 |
| B | Citrate synthase (EC 4.1.3.7) | protein | 370 | 61% helix, 6% strand | Q9LCX9 |
| C | Citrate synthase (EC 4.1.3.7) | protein | 366 | 59% helix, 6% strand | Q9LCX9 |
| D | Citrate synthase (EC 4.1.3.7) | protein | 366 | 60% helix, 6% strand | Q9LCX9 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D
- CIT · Citric acid · additive · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 950 | 0.84 | 0.85 | 116 | empty |
| 2 | 456 | 0.69 | 0.80 | 55 | COA, CIT |
| 3 | 334 | 0.68 | 0.82 | 36 | COA, CIT |
| 4 | 329 | 0.66 | 0.81 | 42 | COA, CIT |
| 5 | 413 | 0.65 | 0.79 | 46 | COA, CIT |
Interfaces
5 interfaces between chains.
- C–D · 4634 Ų buried · 115 hydrogen bonds · protein-protein
- A–B · 4608 Ų buried · 112 hydrogen bonds · protein-protein
- A–C · 411 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 403 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 171 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1IXE · Crystal structure of citrate synthase from Thermus thermophilus HB8 · 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 Q9LCX9
- Elsewhere: RCSB PDB 1IXE · PDBe 1IXE · UniProt Q9LCX9
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