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Structure of citrate synthase from the thermoacidophilic euryarchaeon thermolasma acidophilum
Analyse Structure of citrate synthase from the thermoacidophilic euryarchaeon… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YBO
- Type
- protein
- Length
- 1,553 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Citrate synthase
- EC
- 2.3.3.16
- UniProt
- P21553
- Ligands
- BCT
- Pockets
- 17 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 59% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Citrate synthase (EC 2.3.3.16) | protein | 395 | 58% helix, 5% strand | P21553 |
| B | Citrate synthase (EC 2.3.3.16) | protein | 381 | 58% helix, 6% strand | P21553 |
| C | Citrate synthase (EC 2.3.3.16) | protein | 380 | 59% helix, 6% strand | P21553 |
| D | Citrate synthase (EC 2.3.3.16) | protein | 397 | 59% helix, 5% strand | P21553 |
Ligands and binding sites
- BCT · Bicarbonate ion · ligand · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 378 | 0.71 | 0.83 | 40 | empty |
| 2 | 418 | 0.71 | 0.82 | 39 | empty |
| 3 | 390 | 0.68 | 0.81 | 50 | empty |
| 4 | 380 | 0.66 | 0.80 | 52 | empty |
| 5 | 142 | 0.51 | 0.80 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 4693 Ų buried · 74 hydrogen bonds · protein-protein
- C–D · 4469 Ų buried · 71 hydrogen bonds · protein-protein
- A–D · 1455 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 373 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 328 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4YBO · Structure of Citrate Synthase from the Thermoacidophilic Euryarchaeon Thermolasma… · 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 4YBO · PDBe 4YBO · UniProt P21553
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