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Allosteric modulation of caspase-3 through mutagenesis

Analyse Allosteric modulation of caspase-3 through mutagenesis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4EHL
Type: protein
Length: 471 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-3; ACE-asp-glu-val-asp-chloromethylketone inhibitor
EC: 3.4.22.56
UniProt: P42574
Ligands: ACE, 0QE
Pockets: 1 · best druggability 0.65

Structure

x-ray diffraction · 3 distinct chains · 30% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Caspase-3 (EC 3.4.22.56)	protein	231	30% helix, 28% strand	P42574
C	Caspase-3 (EC 3.4.22.56)	protein	232	31% helix, 27% strand	P42574
B, D	ACE-asp-glu-val-asp-chloromethylketone inhibitor	protein	4	0% helix, 50% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 2 copies · chains A, B, C, D
0QE · Chloromethane · ligand · 2 copies · chains A, B, C, D

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	388	0.65	0.79	41	empty

Interfaces

3 interfaces between chains.

A–C · 2099 Å² buried · 40 hydrogen bonds · protein-protein
C–D · 478 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 475 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

4EHL · Allosteric Modulation of Caspase-3 through Mutagenesis · the same entry in another collection · chain A against A, TM-score 1.00
P42574 · AlphaFold monomer V2.0 prediction for caspase-3 (P42574) · 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 P42574
Elsewhere: RCSB PDB 4EHL · PDBe 4EHL · UniProt P42574

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