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Crystal structure of active caspase-2 bound with ac-vdvad-cho

Analyse Crystal structure of active caspase-2 bound with ac-vdvad-cho in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3R6G
Type: protein
Length: 521 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-2 subunit P18; Caspase-2 subunit P12; Peptide inhibitor (ACE)VDVAD-cho
EC: 3.4.22.55
UniProt: P42575
Ligands: ACE
Pockets: 3 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 30% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Caspase-2 subunit P18 (EC 3.4.22.55)	protein	157	32% helix, 25% strand	P42575
B, D	Caspase-2 subunit P12 (EC 3.4.22.55)	protein	97	28% helix, 20% strand	P42575
C	Caspase-2 subunit P18 (EC 3.4.22.55)	protein	160	30% helix, 24% strand	P42575
F, E	Peptide inhibitor (ACE)VDVAD-cho	protein	5	0% helix, 60% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 2 copies · chains D, F, B, E

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 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	404	0.75	0.85	66	empty
2	130	0.39	0.74	23	empty
3	67	0.36	0.78	17	empty

Interfaces

10 interfaces between chains.

A–B · 2607 Å² buried · 38 hydrogen bonds · protein-protein
C–D · 2594 Å² buried · 39 hydrogen bonds · protein-protein
B–D · 1463 Å² buried · 20 hydrogen bonds · protein-protein
B–C · 461 Å² buried · 12 hydrogen bonds · protein-protein
B–E · 455 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

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

Compared structures

3R6G · Crystal structure of active caspase-2 bound with Ac-VDVAD-CHO · the same entry in another collection · chain E against E, TM-score 1.00
P42575 · AlphaFold monomer V2.0 prediction for caspase-2 (P42575) · 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 P42575
Elsewhere: RCSB PDB 3R6G · PDBe 3R6G · UniProt P42575

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