Research workbench

Caspase 3 V266K

Analyse Caspase 3 V266K in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5IBR
Type: protein
Length: 467 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-3; ACE-asp-glu-val-ask
EC: 3.4.22.56
UniProt: P42574
Ligands: ACE, 0QE
Pockets: 1 · best druggability 0.58

Structure

x-ray diffraction · 3 distinct chains · 30% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Caspase-3 (EC 3.4.22.56)	protein	230	30% helix, 27% strand	P42574
B, D	ACE-asp-glu-val-ask	protein	4	0% helix, 50% strand	—
C	Caspase-3 (EC 3.4.22.56)	protein	229	30% helix, 25% strand	P42574

Ligands and binding sites

ACE · Acetyl group · ligand · 2 copies · chains A, B, C, D
0QE · Chloromethane · ion · 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	242	0.58	0.79	31	empty

Interfaces

3 interfaces between chains.

A–C · 1643 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 469 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 465 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

5IBR · Caspase 3 V266K · the same entry in another collection · chain C against C, TM-score 1.00
P42574 · AlphaFold monomer V2.0 prediction for caspase-3 (P42574) · a predicted model of the same protein · chain A 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 5IBR · PDBe 5IBR · UniProt P42574

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