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Crystal structure of caspase-7 with inhibitor ac-dqmd-cho

Analyse Crystal structure of caspase-7 with inhibitor ac-dqmd-cho in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2QL9
Type: protein
Length: 477 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-7; Inhibitor ac-dqmd-cho; Peptide qghge
EC: 3.4.22.60
UniProt: P55210
Ligands: ACE
Pockets: 1 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 30% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Caspase-7 (EC 3.4.22.60)	protein	140	29% helix, 32% strand	P55210
B, D	Caspase-7 (EC 3.4.22.60)	protein	92	34% helix, 20% strand	P55210
E, F	Inhibitor ac-dqmd-cho	protein	4	0% helix, 50% strand	—
G	Peptide qghge	protein	5	0% helix, 0% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 2 copies · chains B, E, D, F
CIT · Citric acid · additive · chains A, B, C, D

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	513	0.76	0.83	44	CIT

Interfaces

14 interfaces between chains.

A–B · 2306 Å² buried · 35 hydrogen bonds · protein-protein
C–D · 2298 Å² buried · 34 hydrogen bonds · protein-protein
B–D · 1391 Å² buried · 16 hydrogen bonds · protein-protein
D–F · 428 Å² buried · 12 hydrogen bonds · protein-protein
B–E · 420 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

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

Compared structures

2QL9 · Crystal Structure of Caspase-7 with inhibitor AC-DQMD-CHO · the same entry in another collection · chain G against G, 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 2QL9 · PDBe 2QL9 · UniProt P55210

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