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Crystal structure of caspase-3 with inhibitor ac-itakd-cho

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

PDB: 7RNG
Type: protein
Length: 474 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-3 subunit P17; Caspase-3 subunit P12; Ac-itakd-cho
UniProt: P42574
Pockets: 1 · best druggability 0.65

Structure

x-ray diffraction · 3 distinct chains · 30% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Caspase-3 subunit P17	protein	140	28% helix, 29% strand	P42574
B, D	Caspase-3 subunit P12	protein	92	34% helix, 21% strand	P42574
F, G	Ac-itakd-cho	protein	5	0% helix, 60% strand	—

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	297	0.65	0.81	38	empty

Interfaces

10 interfaces between chains.

A–B · 2195 Å² buried · 36 hydrogen bonds · protein-protein
C–D · 2155 Å² buried · 30 hydrogen bonds · protein-protein
B–D · 1425 Å² buried · 18 hydrogen bonds · protein-protein
B–F · 450 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 427 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

7RNG · Crystal structure of caspase-3 with inhibitor Ac-ITAKD-CHO · 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 C 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 7RNG · PDBe 7RNG · UniProt P42574

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