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Structure of the ced-4 apoptosome

Analyse Structure of the ced-4 apoptosome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3LQQ
Type: protein
Length: 1,004 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cell death protein 4
UniProt: P30429
Ligands: ATP, MG
Pockets: 15 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 50% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cell death protein 4	protein	503	50% helix, 9% strand	P30429
B	Cell death protein 4	protein	501	49% helix, 9% strand	P30429

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	703	0.81	0.85	64	MG, ATP
2	1139	0.76	0.78	78	empty
3	367	0.74	0.85	39	MG, ATP
4	263	0.64	0.82	36	empty
5	221	0.59	0.81	27	empty

Interfaces

1 interface between chains.

A–B · 1848 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

3LQQ · Structure of the CED-4 Apoptosome · the same entry in another collection · chain A against A, TM-score 1.00
P30429 · AlphaFold monomer V2.0 prediction for cell death protein 4 (P30429) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 P30429
Elsewhere: RCSB PDB 3LQQ · PDBe 3LQQ · UniProt P30429

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