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Caspase-3 binds diverse P4 residues in peptides

Analyse Caspase-3 binds diverse P4 residues in peptides in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3GJR
Type: protein
Length: 466 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-3 subunit P17; Caspase-3 subunit P12
EC: 3.4.22.56
UniProt: P42574
Ligands: DZE
Pockets: 4 · best druggability 0.66

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Caspase-3 subunit P17 (EC 3.4.22.56)	protein	141	27% helix, 31% strand	P42574
B, D	Caspase-3 subunit P12 (EC 3.4.22.56)	protein	92	34% helix, 18% strand	P42574

Ligands and binding sites

DZE · methyl (3S)-3-[(tert-butoxycarbonyl)amino]-4-oxopentanoate · ligand · 2 copies · chains A, B, C, D
GOL · Glycerol · additive · 2 copies · chains B, D

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	309	0.66	0.81	37	empty
2	136	0.42	0.75	22	DZE, GOL
3	110	0.40	0.76	17	DZE
4	55	0.32	0.76	19	empty

Interfaces

6 interfaces between chains.

A–B · 2236 Å² buried · 32 hydrogen bonds · protein-protein
C–D · 2205 Å² buried · 33 hydrogen bonds · protein-protein
B–D · 1388 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 418 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 407 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

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

Compared structures

3GJR · Caspase-3 Binds Diverse P4 Residues in Peptides · 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 1.00

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 3GJR · PDBe 3GJR · UniProt P42574

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