Research workbench

Structure of the card-card disk

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

PDB: 5WVC
Type: protein
Length: 593 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Apoptotic protease-activating factor 1; Caspase
UniProt: O14727, A8K7U6
Ligands: IOD
Pockets: 3 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 73% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, A	Apoptotic protease-activating factor 1	protein	95	73% helix, 0% strand	O14727
D, B, F	Caspase	protein	103	71% helix, 0% strand	A8K7U6
E	Apoptotic protease-activating factor 1	protein	94	74% helix, 0% strand	O14727

Ligands and binding sites

IOD · Iodide ion · ion · 11 copies · chains C, D, B, E, F

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1117	0.81	0.82	78	IOD
2	249	0.60	0.80	20	empty
3	53	0.46	0.86	18	empty

Interfaces

10 interfaces between chains.

D–E · 626 Å² buried · 12 hydrogen bonds · protein-protein
C–B · 618 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 486 Å² buried · 10 hydrogen bonds · protein-protein
E–F · 478 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 468 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 modified (oxidation).

Compared structures

5WVC · Structure of the CARD-CARD disk · the same entry in another collection · chain F against F, TM-score 1.00
O14727 · AlphaFold monomer V2.0 prediction for apoptotic protease-activating factor 1 (O14727) · a predicted model of the same protein · chain C against A, TM-score 0.98

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 O14727
Every structure of UniProt A8K7U6
Elsewhere: RCSB PDB 5WVC · PDBe 5WVC · UniProt O14727 · UniProt A8K7U6

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