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Caspase-3 mutant - T152A

Analyse Caspase-3 mutant - T152A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6BH9
Type: protein
Length: 488 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, 0QE, NA, CL
Pockets: 3 · best druggability 0.65

Structure

x-ray diffraction · 3 distinct chains · 28% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Caspase-3 (EC 3.4.22.56)	protein	146	26% helix, 31% strand	P42574
C, E	Caspase-3 (EC 3.4.22.56)	protein	94	33% helix, 20% strand	P42574
D, G	Ac-asp-glu-val-asp-cmk	protein	4	0% helix, 50% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 2 copies · chains E, D, C, G
0QE · Chloromethane · ligand · 2 copies · chains B, E, D, A, C, G
NA · Sodium ion · metal · 5 copies · chains A, C, B, E
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

3 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	289	0.65	0.81	35	empty
2	74	0.34	0.76	22	empty
3	73	0.34	0.76	21	empty

Interfaces

10 interfaces between chains.

A–C · 2207 Å² buried · 34 hydrogen bonds · protein-protein
B–E · 2204 Å² buried · 32 hydrogen bonds · protein-protein
C–E · 1476 Å² buried · 21 hydrogen bonds · protein-protein
A–E · 476 Å² buried · 13 hydrogen bonds · protein-protein
C–B · 475 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

6BH9 · Caspase-3 Mutant - T152A · the same entry in another collection · chain G against G, 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 6BH9 · PDBe 6BH9 · UniProt P42574

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