MolNFT v1 · #105091 · protein

Caspase-3 Y195FV266H

4QUE: “Caspase-3 Y195FV266H”. X-ray diffraction, 3 ligands (ACE, 0QE, AZI), 1 pocket (best druggability 0.67). MolNFT v1 #105091 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4QUE
Type: protein
Length: 484 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-3; ACE-asp-glu-val-asp-chloromethylketone inhibitor; Short peptide
EC: 3.4.22.56
UniProt: P42574
Ligands: ACE, 0QE, AZI
Pockets: 1 · best druggability 0.67

Structure

x-ray diffraction · 4 distinct chains · 29% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Caspase-3 (EC 3.4.22.56)	protein	234	29% helix, 27% strand	P42574
C	Caspase-3 (EC 3.4.22.56)	protein	232	29% helix, 27% strand	P42574
H, J	ACE-asp-glu-val-asp-chloromethylketone inhibitor	protein	4	0% helix, 50% strand	—
D, E	Short peptide	protein	5	0% helix, 0% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 2 copies · chains C, H, A, J
0QE · Chloromethane · ion · 2 copies · chains C, H, A, J
AZI · Azide ion · ion · 2 copies · chains A, C
DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains A, J

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	346	0.67	0.81	42	empty

Interfaces

5 interfaces between chains.

A–C · 2237 Å² buried · 44 hydrogen bonds · protein-protein
A–J · 471 Å² buried · 17 hydrogen bonds · protein-protein
C–H · 469 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 336 Å² buried · 9 hydrogen bonds · protein-protein
A–E · 325 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

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

Compared structures

4QUE · Caspase-3 Y195FV266H · the same entry in another collection · chain D against D, 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 4QUE · PDBe 4QUE · UniProt P42574

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