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Crystal strusture of caspase-3 with inhibitor ac-dmqd-cho

Analyse Crystal strusture of caspase-3 with inhibitor ac-dmqd-cho in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2H5J
Type: protein
Length: 477 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-3, P17 subunit; Caspase-3, P12 subunit; Ac-dmqd-cho
EC: 3.4.22.-
UniProt: P42574
Ligands: ACE
Pockets: 2 · best druggability 0.66

Structure

x-ray diffraction · 5 distinct chains · 29% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Caspase-3, P17 subunit (EC 3.4.22.-)	protein	141	27% helix, 32% strand	P42574
B	Caspase-3, P12 subunit (EC 3.4.22.-)	protein	95	33% helix, 20% strand	P42574
C	Caspase-3, P17 subunit (EC 3.4.22.-)	protein	140	28% helix, 32% strand	P42574
D	Caspase-3, P12 subunit (EC 3.4.22.-)	protein	93	33% helix, 20% strand	P42574
E, F	Ac-dmqd-cho	protein	4	0% helix, 50% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 2 copies · chains B, 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	315	0.66	0.81	38	empty
2	78	0.46	0.82	19	empty

Interfaces

10 interfaces between chains.

C–D · 2261 Å² buried · 38 hydrogen bonds · protein-protein
A–B · 2236 Å² buried · 32 hydrogen bonds · protein-protein
B–D · 1354 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 464 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 461 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

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

Compared structures

2H5J · Crystal strusture of caspase-3 with inhibitor Ac-DMQD-Cho · 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 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 2H5J · PDBe 2H5J · UniProt P42574

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