Research workbench

X-ray structure of CARD8 card domain

Analyse X-ray structure of CARD8 card domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4IKM
Type: protein
Length: 463 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Maltose-binding periplasmic protein, caspase recruitment domain-containing protein 8
UniProt: P0AEX9, Q9Y2G2
Ligands: GLC, IOD
Pockets: 7 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 52% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Maltose-binding periplasmic protein, caspase recruitment domain-containing protein 8	protein	463	52% helix, 16% strand	P0AEX9, Q9Y2G2

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
IOD · Iodide ion · ion · 2 copies · chains A
EDO · 1,2-ethanediol · additive · 2 copies · chains A

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

Pockets

7 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	311	0.72	0.85	29	GLC
2	203	0.59	0.81	24	empty
3	69	0.40	0.79	17	empty
4	117	0.36	0.73	19	EDO
5	83	0.32	0.74	17	empty

Modifications

Observed in the structure: 8 modified (nonstandard).

Compared structures

4IKM · X-ray structure of CARD8 CARD domain · the same entry in another collection · chain A against A, TM-score 1.00
Q9Y2G2 · AlphaFold monomer V2.0 prediction for caspase recruitment domain- containing protein 8… · a predicted model of the same protein · chain A against A, TM-score 0.25

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 P0AEX9
Every structure of UniProt Q9Y2G2
Elsewhere: RCSB PDB 4IKM · PDBe 4IKM · UniProt P0AEX9 · UniProt Q9Y2G2

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