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Crystal structure of caspase-3 with peptide inhibitor ac-VDV(DAB)D-cho

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

PDB: 7SEO
Type: protein
Length: 478 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-3 subunit P17; Caspase-3 subunit P12; ACE-val-asp-val-dab-asp
UniProt: P42574
Ligands: ACE
Pockets: 2 · best druggability 0.70

Structure

x-ray diffraction · 5 distinct chains · 29% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Caspase-3 subunit P17	protein	142	26% helix, 31% strand	P42574
B	Caspase-3 subunit P12	protein	93	33% helix, 19% strand	P42574
C	Caspase-3 subunit P17	protein	141	28% helix, 26% strand	P42574
D	Caspase-3 subunit P12	protein	92	33% helix, 20% strand	P42574
F, G	ACE-val-asp-val-dab-asp	protein	5	0% helix, 60% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 2 copies · chains B, F, D, G

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	422	0.70	0.81	43	empty
2	82	0.41	0.78	21	empty

Interfaces

10 interfaces between chains.

A–B · 2258 Å² buried · 33 hydrogen bonds · protein-protein
C–D · 2141 Å² buried · 34 hydrogen bonds · protein-protein
B–D · 1408 Å² buried · 21 hydrogen bonds · protein-protein
B–F · 487 Å² buried · 13 hydrogen bonds · protein-protein
D–G · 479 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

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

Compared structures

7SEO · Crystal Structure of Caspase-3 with Peptide Inhibitor Ac-VDV(DAB)D-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 7SEO · PDBe 7SEO · UniProt P42574

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