Research workbench
X-ray crystal structure of a thiolase from Escherichia coli at 1.8 A resolution
Analyse X-ray crystal structure of a thiolase from Escherichia coli at 1.8 A resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F38
- Type
- protein
- Length
- 1,548 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Escherichia coli K-12
- Molecule
- Acetyl-CoA acetyltransferase
- EC
- 2.3.1.9
- UniProt
- P76461
- Ligands
- 5UG, COZ
- Pockets
- 17 · best druggability 0.64
Structure
x-ray diffraction · resolution 1.9 · 4 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Acetyl-CoA acetyltransferase (EC 2.3.1.9) | protein | 391 | 40% helix, 24% strand | P76461 |
| A | Acetyl-CoA acetyltransferase (EC 2.3.1.9) | protein | 371 | 38% helix, 23% strand | P76461 |
| D | Acetyl-CoA acetyltransferase (EC 2.3.1.9) | protein | 394 | 40% helix, 24% strand | P76461 |
| C | Acetyl-CoA acetyltransferase (EC 2.3.1.9) | protein | 392 | 39% helix, 24% strand | P76461 |
Ligands and binding sites
- 5UG · [(3~{S})-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-4-[[3-oxidanylidene-3-(2-sulfanylethylamino)propyl]amino]butyl] phosphono hydrogen phosphate · ligand · 2 copies · chains A, D, C
- COZ · Coenzyme A · ligand · chains B, C
- EDO · 1,2-ethanediol · additive · 31 copies · chains B, A, D, 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 190 | 0.64 | 0.84 | 31 | EDO |
| 2 | 150 | 0.59 | 0.83 | 28 | 5UG |
| 3 | 141 | 0.59 | 0.83 | 22 | EDO |
| 4 | 164 | 0.59 | 0.82 | 27 | EDO |
| 5 | 139 | 0.58 | 0.83 | 27 | empty |
Interfaces
6 interfaces between chains.
- D–C · 2671 Ų buried · 61 hydrogen bonds · protein-protein
- B–A · 2522 Ų buried · 58 hydrogen bonds · protein-protein
- A–D · 723 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 717 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 305 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (methylation, oxidation).
Compared structures
- 5F38 · X-ray crystal structure of a thiolase from escherichia COLI at 1.8 a resolution · the same entry in another collection · chain D against D, TM-score 1.00
- P76461 · AlphaFold monomer V2.0 prediction for acetyl-CoA acetyltransferase (P76461) · a predicted model of the same protein · 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 P76461
- Elsewhere: RCSB PDB 5F38 · PDBe 5F38 · UniProt P76461
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