MolNFT v1 · #105093 · protein

Caspase-3 M61A

4QUG: “Caspase-3 M61A”. X-ray diffraction, 4 ligands (ACE, AZI, 0QE), 1 pocket (best druggability 0.66). MolNFT v1 #105093 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4QUG
Type: protein
Length: 472 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, AZI, 0QE, CL
Pockets: 1 · best druggability 0.66

Structure

x-ray diffraction · 2 distinct chains · 29% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Caspase-3 (EC 3.4.22.56)	protein	232	30% helix, 28% strand	P42574
D, B	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, D, C, B
AZI · Azide ion · ion · 3 copies · chains A, C
0QE · Chloromethane · ion · 2 copies · chains A, D, C, B
CL · Chloride ion · ion · chains A, C
ACT · Acetate ion · additive · chains A, 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	310	0.66	0.81	38	empty

Interfaces

3 interfaces between chains.

A–C · 2175 Å² buried · 36 hydrogen bonds · protein-protein
A–D · 466 Å² buried · 13 hydrogen bonds · protein-protein
C–B · 465 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

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

Compared structures

4QUG · Caspase-3 M61A · 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 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 4QUG · PDBe 4QUG · UniProt P42574

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