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Caspase-7 in complex with ketomethylene inhibitor reveals tetrahedral adduct

Analyse Caspase-7 in complex with ketomethylene inhibitor reveals tetrahedral adduct in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6X8J
Type: protein
Length: 470 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-7; Ketomethylene inhibitor
EC: 3.4.22.60
UniProt: P55210
Ligands: ACE
Pockets: 1 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 31% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Caspase-7 (EC 3.4.22.60)	protein	140	29% helix, 33% strand	P55210
C, D	Caspase-7 (EC 3.4.22.60)	protein	91	34% helix, 21% strand	P55210
E, F	Ketomethylene inhibitor	protein	4	0% helix, 50% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 2 copies · chains C, 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	566	0.74	0.81	42	empty

Interfaces

10 interfaces between chains.

A–C · 2229 Å² buried · 36 hydrogen bonds · protein-protein
B–D · 2224 Å² buried · 33 hydrogen bonds · protein-protein
C–D · 1357 Å² buried · 14 hydrogen bonds · protein-protein
C–E · 433 Å² buried · 11 hydrogen bonds · protein-protein
D–F · 420 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

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

Compared structures

6X8J · Caspase-7 in complex with ketomethylene inhibitor reveals tetrahedral adduct · the same entry in another collection · chain C against C, TM-score 1.00
P55210 · AlphaFold monomer V2.0 prediction for caspase-7 (P55210) · a predicted model of the same protein · chain B 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 6X8J · PDBe 6X8J · UniProt P55210

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