MolNFT v1 · #50134 · protein
The structure of the binary complex of citryl dethia CoA and citrate synthase from the thermophilic archaeonthermoplasma acidophilum
2R9E: “The structure of the binary complex of citryl dethia CoA and citrate synthase from the thermophilic…”. X-ray diffraction, 1 ligand (SDX), 14 pockets (best druggability 0.74). MolNFT v1 #50134 on GenesisL1: 3D structure, binding…
- 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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