Research workbench

Human procaspase-3 bound to ac-devd-cmk

Analyse Human procaspase-3 bound to ac-devd-cmk in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4JR0
Type: protein
Length: 460 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Procaspase-3; Ac-devd-cmk
EC: 3.4.22.56
UniProt: P42574
Ligands: ACE, 0QE, CL
Pockets: 4 · best druggability 0.64

Structure

x-ray diffraction · 3 distinct chains · 31% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Procaspase-3 (EC 3.4.22.56)	protein	226	31% helix, 25% strand	P42574
B	Procaspase-3 (EC 3.4.22.56)	protein	226	32% helix, 25% strand	P42574
C, D	Ac-devd-cmk	protein	4	0% helix, 50% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 2 copies · chains A, C, B, D
0QE · Chloromethane · ion · 2 copies · chains A, C, B, D
CL · Chloride ion · ion · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	325	0.64	0.80	28	empty
2	55	0.40	0.81	14	empty
3	65	0.34	0.76	16	empty
4	68	0.32	0.75	14	empty

Interfaces

3 interfaces between chains.

A–B · 1417 Å² buried · 26 hydrogen bonds · protein-protein
A–C · 482 Å² buried · 17 hydrogen bonds · protein-protein
B–D · 477 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

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

Compared structures

4JR0 · Human procaspase-3 bound to Ac-DEVD-CMK · 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 0.98

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 4JR0 · PDBe 4JR0 · UniProt P42574

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