MolNFT v1 · #66589 · protein

High-resolution structure of the extracellular domain of human CD69

3HUP · Early activation antigen CD69: “High-resolution structure of the extracellular domain of human CD69”. X-ray diffraction, 2 ligands (NA, CL), 2 pockets (best druggability 0.39). MolNFT v1 #66589 on GenesisL1: 3D structure, binding…

PDB: 3HUP
Type: protein
Length: 239 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Early activation antigen CD69
UniProt: Q07108
Ligands: NA, CL
Pockets: 2 · best druggability 0.39

Structure

x-ray diffraction · 2 distinct chains · 17% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Early activation antigen CD69	protein	121	17% helix, 34% strand	Q07108
B	Early activation antigen CD69	protein	118	17% helix, 33% strand	Q07108

Ligands and binding sites

NA · Sodium ion · metal · chains A, B
CL · Chloride ion · ion · 5 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	136	0.39	0.73	24	empty
2	111	0.38	0.75	21	empty

Interfaces

1 interface between chains.

A–B · 990 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

3HUP · High-resolution structure of the extracellular domain of human CD69 · the same entry in another collection · chain A against A, TM-score 1.00
Q07108 · AlphaFold monomer V2.0 prediction for early activation antigen CD69 (Q07108) · a predicted model of the same protein · chain B 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 Q07108
Elsewhere: RCSB PDB 3HUP · PDBe 3HUP · UniProt Q07108

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