Research workbench

Caspase-7 in complex with ac-DW3-ke

Analyse Caspase-7 in complex with ac-DW3-ke in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6CL1
Type: protein
Length: 468 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-B3L-phe-1U8
EC: 3.4.22.60
UniProt: P55210
Pockets: 1 · best druggability 0.71

Structure

x-ray diffraction · 3 distinct chains · 32% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Caspase-7 subunit P20 (EC 3.4.22.60)	protein	140	31% helix, 27% 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-B3L-phe-1U8	protein	3	0% helix, 33% 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	503	0.71	0.80	47	empty

Interfaces

10 interfaces between chains.

C–D · 2253 Å² buried · 36 hydrogen bonds · protein-protein
A–B · 2210 Å² buried · 33 hydrogen bonds · protein-protein
B–D · 1337 Å² buried · 17 hydrogen bonds · protein-protein
A–D · 371 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 336 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (nonstandard).

Compared structures

6CL1 · Caspase-7 in complex with Ac-DW3-KE · the same entry in another collection · chain B against B, 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 6CL1 · PDBe 6CL1 · UniProt P55210

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