Research workbench

Caspase-3 T140G

Analyse Caspase-3 T140G in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4QUH
Type: protein
Length: 480 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-3; Short peptde; ACE-asp-glu-val-asp-chloromethylketone inhibitor
EC: 3.4.22.56
UniProt: P42574
Ligands: ACE, AZI, 0QE
Pockets: 1 · best druggability 0.68

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Caspase-3 (EC 3.4.22.56)	protein	233	28% helix, 27% strand	P42574
C	Caspase-3 (EC 3.4.22.56)	protein	234	29% helix, 27% strand	P42574
D	Short peptde	protein	5	0% helix, 0% strand	—
I, J	ACE-asp-glu-val-asp-chloromethylketone inhibitor	protein	4	0% helix, 50% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 2 copies · chains C, I, A, J
AZI · Azide ion · ion · 4 copies · chains A, C
0QE · Chloromethane · ion · 2 copies · chains C, I, A, J
MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains A, C
DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains C

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	374	0.68	0.81	37	MRD

Interfaces

4 interfaces between chains.

A–C · 2211 Å² buried · 46 hydrogen bonds · protein-protein
A–J · 475 Å² buried · 15 hydrogen bonds · protein-protein
C–I · 467 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 252 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

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

Compared structures

4QUH · Caspase-3 T140G · 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 4QUH · PDBe 4QUH · UniProt P42574

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