Research workbench

Caspase-7 in complex with ac-ATS009-ke

Analyse Caspase-7 in complex with ac-ATS009-ke in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6CL2
Type: protein
Length: 472 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-7 subunit P20; Caspase-7 subunit P11; ACE-1MH-asp-PF5-phe-1U8
EC: 3.4.22.60
UniProt: P55210
Ligands: ACE
Pockets: 1 · best druggability 0.72

Structure

x-ray diffraction · 3 distinct chains · 31% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Caspase-7 subunit P20 (EC 3.4.22.60)	protein	140	31% helix, 32% strand	P55210
B, D	Caspase-7 subunit P11 (EC 3.4.22.60)	protein	91	34% helix, 20% strand	P55210
E, F	ACE-1MH-asp-PF5-phe-1U8	protein	5	0% helix, 40% 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

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	507	0.72	0.81	40	empty

Interfaces

10 interfaces between chains.

C–D · 2228 Å² buried · 35 hydrogen bonds · protein-protein
A–B · 2211 Å² buried · 34 hydrogen bonds · protein-protein
B–D · 1348 Å² buried · 17 hydrogen bonds · protein-protein
D–F · 505 Å² buried · 10 hydrogen bonds · protein-protein
B–E · 491 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 modified, 2 covalent (nonstandard, covalent ligand).

Compared structures

6CL2 · Caspase-7 in complex with Ac-ATS009-KE · the same entry in another collection · chain F against F, TM-score 1.00
P55210 · AlphaFold monomer V2.0 prediction for caspase-7 (P55210) · 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 P55210
Elsewhere: RCSB PDB 6CL2 · PDBe 6CL2 · UniProt P55210

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