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: 2IBY
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: 12 · best druggability 0.58

Structure

x-ray diffraction · 2 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, D	Acetyl-CoA acetyltransferase (EC 2.3.1.9)	protein	393	38% helix, 25% strand	P24752

Ligands and binding sites

COA · Coenzyme A · ligand · 4 copies · chains A, B, D, C
K · Potassium ion · metal · 4 copies · chains A, B, C, D
CL · Chloride ion · ion · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 2 copies · chains A, B
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	188	0.58	0.81	34	COA
2	195	0.57	0.80	34	COA
3	199	0.57	0.80	33	COA
4	184	0.57	0.80	33	COA
5	224	0.51	0.76	35	empty

Interfaces

6 interfaces between chains.

C–D · 2776 Å² buried · 57 hydrogen bonds · protein-protein
A–B · 2692 Å² buried · 57 hydrogen bonds · protein-protein
B–D · 622 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 612 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 327 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (oxidation).

Compared structures

2IBY · 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 2IBY · PDBe 2IBY · UniProt P24752

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.