Research workbench

Caspase-3 in complex with elongated ketomethylene inhibitor

Analyse Caspase-3 in complex with elongated ketomethylene inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6X8K
Type: protein
Length: 476 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-3; Ketomethylene inhibitor
EC: 3.4.22.56
UniProt: P42574
Ligands: ACE
Pockets: 2 · best druggability 0.52

Structure

x-ray diffraction · 5 distinct chains · 30% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Caspase-3 (EC 3.4.22.56)	protein	140	29% helix, 32% strand	P42574
B	Caspase-3 (EC 3.4.22.56)	protein	140	28% helix, 32% strand	P42574
C	Caspase-3 (EC 3.4.22.56)	protein	90	34% helix, 20% strand	P42574
D	Caspase-3 (EC 3.4.22.56)	protein	92	34% helix, 20% strand	P42574
E, F	Ketomethylene inhibitor	protein	7	0% helix, 29% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 2 copies · chains C, E, 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	283	0.52	0.74	44	empty
2	72	0.31	0.74	17	empty

Interfaces

9 interfaces between chains.

B–D · 2161 Å² buried · 33 hydrogen bonds · protein-protein
A–C · 2112 Å² buried · 28 hydrogen bonds · protein-protein
D–F · 463 Å² buried · 13 hydrogen bonds · protein-protein
C–E · 453 Å² buried · 12 hydrogen bonds · protein-protein
B–F · 348 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

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

Compared structures

6X8K · Caspase-3 in complex with elongated ketomethylene inhibitor · the same entry in another collection · chain B against B, TM-score 1.00
P42574 · AlphaFold monomer V2.0 prediction for caspase-3 (P42574) · a predicted model of the same protein · chain B 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 6X8K · PDBe 6X8K · UniProt P42574

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