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The structure of the binary complex of oxalateacetate with citrate synthase from the thermophilic archaeon thermolasma acidophilum
Analyse The structure of the binary complex of oxalateacetate with citrate synthase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IFC
- 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
- OAA
- Pockets
- 13 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 60% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Citrate synthase (EC 2.3.3.1) | protein | 380 | 60% helix, 6% strand | P21553 |
| C | Citrate synthase (EC 2.3.3.1) | protein | 382 | 60% helix, 6% strand | P21553 |
| D | Citrate synthase (EC 2.3.3.1) | protein | 376 | 59% helix, 6% strand | P21553 |
Ligands and binding sites
- OAA · Oxaloacetate ion · ligand · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 288 | 0.69 | 0.84 | 33 | OAA |
| 2 | 253 | 0.68 | 0.84 | 32 | OAA |
| 3 | 292 | 0.66 | 0.82 | 33 | OAA |
| 4 | 315 | 0.66 | 0.81 | 32 | OAA |
| 5 | 83 | 0.48 | 0.82 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–C · 4699 Ų buried · 86 hydrogen bonds · protein-protein
- B–D · 4611 Ų buried · 85 hydrogen bonds · protein-protein
Compared structures
- 2IFC · The Structure of the Binary Complex of Oxalateacetate with 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 C against A, TM-score 0.99
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 2IFC · PDBe 2IFC · UniProt P21553
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