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Crystal structure of caspase-3 with inhibitor ac-ldesd-cho

Analyse Crystal structure of caspase-3 with inhibitor ac-ldesd-cho in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3EDQ
Type: protein
Length: 477 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-3; Ac-ldesd-cho peptide
EC: 3.4.22.56
UniProt: P42574
Ligands: ACE
Pockets: 1 · best druggability 0.65

Structure

x-ray diffraction · 4 distinct chains · 27% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Caspase-3 (EC 3.4.22.56)	protein	140	27% helix, 29% strand	P42574
B, D	Caspase-3 (EC 3.4.22.56)	protein	93	33% helix, 19% strand	P42574
C	Caspase-3 (EC 3.4.22.56)	protein	141	25% helix, 31% strand	P42574
E, F	Ac-ldesd-cho peptide	protein	5	0% helix, 60% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 2 copies · chains B, E, D, F

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	319	0.65	0.80	36	empty

Interfaces

10 interfaces between chains.

A–B · 2235 Å² buried · 37 hydrogen bonds · protein-protein
C–D · 2202 Å² buried · 35 hydrogen bonds · protein-protein
B–D · 1400 Å² buried · 19 hydrogen bonds · protein-protein
D–F · 493 Å² buried · 15 hydrogen bonds · protein-protein
B–E · 486 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent, 2 modified (covalent ligand, nonstandard).

Compared structures

3EDQ · Crystal structure of Caspase-3 with inhibitor AC-LDESD-CHO · the same entry in another collection · chain F against F, 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 3EDQ · PDBe 3EDQ · UniProt P42574

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