Research workbench

Crystal structure of the C-terminal domain of mouse TLR9

Analyse Crystal structure of the C-terminal domain of mouse TLR9 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4QDH
Type: protein
Length: 795 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Variable lymphocyte receptor B, toll-like receptor 9 chimera
UniProt: Q4G1L2, Q9EQU3
Ligands: NAG, SO4
Pockets: 8 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 11% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Variable lymphocyte receptor B, toll-like receptor 9 chimera	protein	402	11% helix, 15% strand	Q4G1L2, Q9EQU3
B	Variable lymphocyte receptor B, toll-like receptor 9 chimera	protein	393	11% helix, 16% strand	Q4G1L2, Q9EQU3

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
SO4 · Sulfate ion · ion · 8 copies · chains A, B

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

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	956	0.76	0.79	100	SO4
2	193	0.60	0.81	28	empty
3	188	0.57	0.80	27	empty
4	218	0.55	0.77	22	empty
5	73	0.51	0.85	20	empty

Interfaces

1 interface between chains.

A–B · 1527 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 glycan, 8 disulfide (N-glycosylation, disulfide).

Compared structures

4QDH · Crystal Structure of the C-terminal Domain of Mouse TLR9 · the same entry in another collection · chain A against A, TM-score 1.00
Q9EQU3 · AlphaFold monomer V2.0 prediction for toll-like receptor 9 (Q9EQU3) · a predicted model of the same protein · chain B against A, TM-score 0.85

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 Q4G1L2
Every structure of UniProt Q9EQU3
Elsewhere: RCSB PDB 4QDH · PDBe 4QDH · UniProt Q4G1L2 · UniProt Q9EQU3

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.