Research workbench

Caspase-3 mutant - D9A,D28A,S150D

Analyse Caspase-3 mutant - D9A,D28A,S150D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6BG0
Type: protein
Length: 476 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-3; Ac-asp-glu-val-asp-cmk
EC: 3.4.22.56
UniProt: P42574
Ligands: ACE, NA, AZI, 0QE
Pockets: 2 · best druggability 0.67

Structure

x-ray diffraction · 3 distinct chains · 29% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Caspase-3 (EC 3.4.22.56)	protein	141	28% helix, 29% strand	P42574
C, D	Caspase-3 (EC 3.4.22.56)	protein	93	33% helix, 20% strand	P42574
G, F	Ac-asp-glu-val-asp-cmk	protein	4	0% helix, 50% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 2 copies · chains C, G, D, F
NA · Sodium ion · metal · 2 copies · chains A, C, B, D
AZI · Azide ion · ion · 3 copies · chains A, C, B, D, G
0QE · Chloromethane · ion · 2 copies · chains A, C, G, B, D, F

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

Pockets

2 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	298	0.67	0.82	46	empty
2	55	0.34	0.77	18	empty

Interfaces

10 interfaces between chains.

B–D · 2180 Å² buried · 32 hydrogen bonds · protein-protein
A–C · 2158 Å² buried · 34 hydrogen bonds · protein-protein
C–D · 1460 Å² buried · 21 hydrogen bonds · protein-protein
A–D · 442 Å² buried · 11 hydrogen bonds · protein-protein
C–B · 433 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

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

Compared structures

6BG0 · Caspase-3 Mutant - D9A,D28A,S150D · 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 A 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 6BG0 · PDBe 6BG0 · UniProt P42574

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