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Crystal Structure of caspase 3, L168F mutant

Analyse Crystal Structure of caspase 3, L168F mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4DCP
Type: protein
Length: 478 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.7
Source: Homo sapiens; SYNTHETIC CONSTRUCT
Molecule: Caspase-3 subunit p17; Caspase-3 subunit p12; Caspase Inhibitor AC-DEVD-CHO
EC: 3.4.22.56
UniProt: P42574
Pockets: 1 · best druggability 0.65

Structure

x-ray diffraction · resolution 1.7 · 4 distinct chains · 30% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Caspase-3 subunit p17 (EC 3.4.22.56)	protein	141	27% helix, 32% strand	P42574
B	Caspase-3 subunit p12 (EC 3.4.22.56)	protein	95	33% helix, 20% strand	P42574
C, F	Caspase Inhibitor AC-DEVD-CHO	protein	4	0% helix, 50% strand	—
E	Caspase-3 subunit p12 (EC 3.4.22.56)	protein	93	33% helix, 20% strand	P42574

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	303	0.65	0.81	33	empty

Interfaces

10 interfaces between chains.

A–B · 2238 Å² buried · 35 hydrogen bonds · protein-protein
D–E · 2206 Å² buried · 34 hydrogen bonds · protein-protein
B–E · 1417 Å² buried · 19 hydrogen bonds · protein-protein
A–E · 444 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 418 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (nonstandard).

Compared structures

4DCP · Crystal structure of caspase 3, L168F mutant · the same entry in another collection · chain F against F, TM-score 1.00
P42574 · AlphaFold monomer V2.0 prediction for caspase-3 (P42574) · a predicted model of the same protein · chain D 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 4DCP · PDBe 4DCP · UniProt P42574

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