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Crystal structure of ced-4 bound ced-3 fragment

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

PDB: 4M9Z
Type: protein
Length: 2,064 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cell death protein 4; Ced-3 fragment
UniProt: P30429
Ligands: ATP, MG
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 5 distinct chains · 50% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Cell death protein 4	protein	510	51% helix, 9% strand	P30429
E	Ced-3 fragment	protein	6	50% helix, 17% strand	—
B, D	Cell death protein 4	protein	511	50% helix, 9% strand	P30429
F, G	Ced-3 fragment	protein	5	0% helix, 0% strand	—
H	Ced-3 fragment	protein	6	0% helix, 0% strand	—

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	707	0.81	0.85	59	MG, ATP
2	1100	0.81	0.82	89	MG, ATP
3	877	0.76	0.79	69	empty
4	767	0.74	0.80	55	empty
5	328	0.73	0.85	37	MG, ATP

Interfaces

8 interfaces between chains.

C–D · 1913 Å² buried · 28 hydrogen bonds · protein-protein
A–B · 1893 Å² buried · 30 hydrogen bonds · protein-protein
B–C · 430 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 418 Å² buried · 2 hydrogen bonds · protein-protein
A–E · 413 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 72 modified (engineered).

Compared structures

4M9Z · Crystal structure of CED-4 bound CED-3 fragment · the same entry in another collection · chain H against H, 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 0.97

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 4M9Z · PDBe 4M9Z · UniProt P30429

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