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Crystal structure of the the CD9

Analyse Crystal structure of the the CD9 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6K4J
Type: protein
Length: 220 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CD9 antigen
UniProt: P21926
Ligands: PLM, NI
Pockets: 3 · best druggability 0.53

Structure

x-ray diffraction · 1 distinct chain · 79% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	CD9 antigen	protein	220	79% helix, 1% strand	P21926

Ligands and binding sites

PLM · Palmitic acid · ligand · chains A
NI · Nickel (II) ion · metal · chains A
OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	162	0.53	0.78	19	empty
2	112	0.46	0.78	21	empty
3	61	0.27	0.72	12	empty

Modifications

Observed in the structure: 2 disulfide, 1 lipid (disulfide, palmitoylation).

Compared structures

6K4J · Crystal Structure of the the CD9 · the same entry in another collection · chain A against A, TM-score 1.00
P21926 · AlphaFold monomer V2.0 prediction for CD9 antigen (P21926) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P21926
Elsewhere: RCSB PDB 6K4J · PDBe 6K4J · UniProt P21926

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