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

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

PDB: 7RNF
Type: protein
Length: 472 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-vdkvd-cho
UniProt: P42574
Ligands: ACE
Pockets: 1 · best druggability 0.65

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Caspase-3 subunit P17	protein	140	27% helix, 31% strand	P42574
B	Caspase-3 subunit P12	protein	91	34% helix, 20% strand	P42574
C	Caspase-3 subunit P17	protein	139	28% helix, 32% strand	P42574
D	Caspase-3 subunit P12	protein	92	34% helix, 20% strand	P42574
F, G	Ac-vdkvd-cho	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

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	321	0.65	0.80	36	empty

Interfaces

10 interfaces between chains.

C–D · 2163 Å² buried · 35 hydrogen bonds · protein-protein
A–B · 2159 Å² buried · 32 hydrogen bonds · protein-protein
B–D · 1399 Å² buried · 20 hydrogen bonds · protein-protein
D–G · 482 Å² buried · 12 hydrogen bonds · protein-protein
B–F · 472 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

7RNF · Crystal structure of caspase-3 with inhibitor Ac-VDKVD-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 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 7RNF · PDBe 7RNF · UniProt P42574

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