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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: 4M9Y
Type: protein
Length: 1,033 residues
Chains: 4
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: 16 · best druggability 0.80

Structure

x-ray diffraction · 4 distinct chains · 51% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cell death protein 4	protein	510	51% helix, 9% strand	P30429
C	Ced-3 fragment	protein	7	0% helix, 0% strand	—
B	Cell death protein 4	protein	511	52% helix, 9% strand	P30429
D	Ced-3 fragment	protein	5	0% helix, 0% strand	—

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

16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	691	0.80	0.84	59	MG, ATP
2	872	0.74	0.78	61	empty
3	869	0.74	0.78	88	empty
4	318	0.74	0.86	38	MG, ATP
5	339	0.60	0.77	34	empty

Interfaces

3 interfaces between chains.

A–B · 1876 Å² buried · 27 hydrogen bonds · protein-protein
B–D · 413 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 405 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 36 modified (engineered).

Compared structures

4M9Y · Crystal structure of CED-4 bound CED-3 fragment · 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 4M9Y · PDBe 4M9Y · UniProt P30429

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