Research workbench
Crystallographic and kinetic studies of human mitochondrial acetoacetyl-CoA thiolase (T2): the importance of potassium and chloride for its structure and function
Analyse Crystallographic and kinetic studies of human mitochondrial acetoacetyl-CoA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IBW
- Type
- protein
- Length
- 1,568 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetyl-CoA acetyltransferase
- EC
- 2.3.1.9
- UniProt
- P24752
- Ligands
- COA, K, CL
- Pockets
- 14 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Acetyl-CoA acetyltransferase (EC 2.3.1.9) | protein | 391 | 38% helix, 25% strand | P24752 |
| C, D | Acetyl-CoA acetyltransferase (EC 2.3.1.9) | protein | 393 | 39% helix, 25% strand | P24752 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, C
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.59 | 0.84 | 25 | empty |
| 2 | 188 | 0.58 | 0.80 | 34 | COA |
| 3 | 130 | 0.57 | 0.83 | 23 | empty |
| 4 | 202 | 0.56 | 0.79 | 36 | COA, MES |
| 5 | 215 | 0.51 | 0.76 | 33 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2787 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 2732 Ų buried · 52 hydrogen bonds · protein-protein
- B–D · 610 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 601 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 329 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 2IBW · Crystallographic and kinetic studies of human mitochondrial acetoacetyl-CoA thiolase… · the same entry in another collection · chain A against A, TM-score 1.00
- P24752 · AlphaFold monomer V2.0 prediction for acetyl-CoA acetyltransferase, mitochondrial (P24752) · a predicted model of the same protein · chain C 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 P24752
- Elsewhere: RCSB PDB 2IBW · PDBe 2IBW · UniProt P24752
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