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CASPASE2 in complex with chdi ligand 33C

Analyse CASPASE2 in complex with chdi ligand 33C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3RJM
Type: protein
Length: 523 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-2; Peptide inhibitor (ACE)VDV(3PX)D-cho
EC: 3.4.22.55
UniProt: P42575
Ligands: ACE
Pockets: 4 · best druggability 0.80

Structure

x-ray diffraction · 5 distinct chains · 29% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Caspase-2 (EC 3.4.22.55)	protein	159	31% helix, 25% strand	P42575
B	Caspase-2 (EC 3.4.22.55)	protein	97	28% helix, 18% strand	P42575
C	Caspase-2 (EC 3.4.22.55)	protein	160	29% helix, 24% strand	P42575
D	Caspase-2 (EC 3.4.22.55)	protein	97	28% helix, 20% strand	P42575
E, F	Peptide inhibitor (ACE)VDV(3PX)D-cho	protein	5	0% helix, 60% 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

4 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	347	0.80	0.90	43	empty
2	86	0.40	0.78	19	empty
3	80	0.31	0.73	19	empty
4	50	0.27	0.74	13	empty

Interfaces

10 interfaces between chains.

C–D · 2649 Å² buried · 40 hydrogen bonds · protein-protein
A–B · 2629 Å² buried · 37 hydrogen bonds · protein-protein
B–D · 1404 Å² buried · 22 hydrogen bonds · protein-protein
B–E · 500 Å² buried · 12 hydrogen bonds · protein-protein
D–F · 499 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified, 2 covalent, 1 disulfide (nonstandard, covalent ligand, disulfide).

Compared structures

3RJM · CASPASE2 IN COMPLEX WITH CHDI LIGAND 33c · the same entry in another collection · chain F against F, TM-score 1.00
P42575 · AlphaFold monomer V2.0 prediction for caspase-2 (P42575) · 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 P42575
Elsewhere: RCSB PDB 3RJM · PDBe 3RJM · UniProt P42575

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