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The structure of the binary complex of citryl dethia CoA and citrate synthase from the thermophilic archaeonthermoplasma acidophilum
Analyse The structure of the binary complex of citryl dethia CoA and citrate synthase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R9E
- Type
- protein
- Length
- 1,518 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Citrate synthase
- EC
- 2.3.3.1
- UniProt
- P21553
- Ligands
- SDX
- Pockets
- 14 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Citrate synthase (EC 2.3.3.1) | protein | 381 | 59% helix, 6% strand | P21553 |
| B, C, D | Citrate synthase (EC 2.3.3.1) | protein | 379 | 60% helix, 6% strand | P21553 |
Ligands and binding sites
- SDX · s-citryldethia Coenzyme A · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 775 | 0.74 | 0.79 | 74 | empty |
| 2 | 277 | 0.70 | 0.84 | 34 | SDX |
| 3 | 310 | 0.70 | 0.84 | 36 | SDX |
| 4 | 292 | 0.69 | 0.84 | 35 | SDX |
| 5 | 285 | 0.68 | 0.83 | 35 | SDX |
Interfaces
5 interfaces between chains.
- C–D · 4722 Ų buried · 88 hydrogen bonds · protein-protein
- A–B · 4681 Ų buried · 94 hydrogen bonds · protein-protein
- B–C · 223 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 167 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 106 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2R9E · The structure of the binary complex of citryl dethia COA and citrate synthase from the… · the same entry in another collection · chain D against D, TM-score 1.00
- P21553 · AlphaFold monomer V2.0 prediction for citrate synthase (P21553) · a predicted model of the same protein · chain D against A, TM-score 0.97
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 P21553
- Elsewhere: RCSB PDB 2R9E · PDBe 2R9E · UniProt P21553
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