Research workbench

Caspase-3 specific unnatural amino acid peptides

Analyse Caspase-3 specific unnatural amino acid peptides in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4JJ8
Type: protein
Length: 472 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-7; Caspase inhibitor
EC: 3.4.22.60
UniProt: P55210
Ligands: ACE
Pockets: 2 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Caspase-7 (EC 3.4.22.60)	protein	231	32% helix, 27% strand	P55210
C, D	Caspase inhibitor	protein	5	0% helix, 20% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 2 copies · chains C, D

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	532	0.72	0.80	53	empty
2	76	0.39	0.78	18	empty

Interfaces

3 interfaces between chains.

A–B · 1971 Å² buried · 31 hydrogen bonds · protein-protein
B–D · 456 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 436 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified, 2 covalent (nonstandard, covalent ligand).

Compared structures

4JJ8 · Caspase-3 specific unnatural amino acid peptides · the same entry in another collection · chain A against A, TM-score 1.00
P55210 · AlphaFold monomer V2.0 prediction for caspase-7 (P55210) · a predicted model of the same protein · chain A 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 P55210
Elsewhere: RCSB PDB 4JJ8 · PDBe 4JJ8 · UniProt P55210

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