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Crystal structure of bovine TLR9 in complex with agonistic DNA1668_12MER

Analyse Crystal structure of bovine TLR9 in complex with agonistic DNA1668_12MER in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3WPE
Type: protein + DNA
Length: 720 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Toll-like receptor 9; DNA (5'-D(*CP*AP*TP*GP*AP*CP*GP*TP*TP*CP*CP*T)-3')
UniProt: Q5I2M5
Pockets: 2 · best druggability 0.56

Structure

x-ray diffraction · 2 distinct chains · 10% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Toll-like receptor 9	protein	714	10% helix, 17% strand	Q5I2M5
C	DNA (5'-D(CPAPTPGPAPCPGPTPTPCPCPT)-3')	dna	6	—	—

Pockets

2 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	66	0.56	0.88	20	empty
2	177	0.43	0.73	19	empty

Interfaces

1 interface between chains.

A–C · 727 Å² buried · 10 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

3WPE · Crystal structure of bovine TLR9 in complex with agonistic DNA1668_12mer · the same entry in another collection · chain A against A, TM-score 1.00
Q5I2M5 · AlphaFold monomer V2.0 prediction for toll-like receptor 9 (Q5I2M5) · 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 Q5I2M5
Elsewhere: RCSB PDB 3WPE · PDBe 3WPE · UniProt Q5I2M5

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