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
- 2IB7
- Type
- protein
- Length
- 1,567 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
- CL
- Pockets
- 13 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Acetyl-CoA acetyltransferase (EC 2.3.1.9) | protein | 391 | 39% helix, 25% strand | P24752 |
| C | Acetyl-CoA acetyltransferase (EC 2.3.1.9) | protein | 392 | 38% helix, 26% strand | P24752 |
| D | Acetyl-CoA acetyltransferase (EC 2.3.1.9) | protein | 393 | 37% helix, 24% strand | P24752 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 copies · chains A, B, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 176 | 0.58 | 0.81 | 36 | empty |
| 2 | 187 | 0.57 | 0.80 | 34 | GOL |
| 3 | 167 | 0.56 | 0.81 | 34 | GOL |
| 4 | 171 | 0.56 | 0.80 | 35 | GOL |
| 5 | 213 | 0.52 | 0.77 | 35 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2783 Ų buried · 61 hydrogen bonds · protein-protein
- A–B · 2708 Ų buried · 54 hydrogen bonds · protein-protein
- A–C · 629 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 604 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 325 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2IB7 · 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 2IB7 · PDBe 2IB7 · UniProt P24752
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