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Crystal structure of human TLR8 in complex with CU-CPT9c

Analyse Crystal structure of human TLR8 in complex with CU-CPT9c in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5Z15
Type: protein
Length: 1,481 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.9
Source: Homo sapiens
Molecule: Toll-like receptor 8
UniProt: Q9NR97
Ligands: 7VL, NAG, MAN, BMA
Pockets: 16 · best druggability 0.78

Structure

x-ray diffraction · resolution 2.9 · 2 distinct chains · 9% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Toll-like receptor 8	protein	743	10% helix, 16% strand	Q9NR97
B	Toll-like receptor 8	protein	738	9% helix, 16% strand	Q9NR97

Ligands and binding sites

7VL · 4-(7-chloranylquinolin-4-yl)-2-methyl-phenol · ligand · 2 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B
MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A
BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B

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

Pockets

16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	655	0.78	0.83	90	NAG, 7VL
2	1037	0.76	0.78	106	NAG
3	231	0.74	0.89	30	7VL
4	343	0.62	0.78	50	empty
5	261	0.61	0.79	28	NAG

Interfaces

1 interface between chains.

A–B · 1627 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 10 glycan (disulfide, N-glycosylation).

Compared structures

5Z15 · Crystal structure of human TLR8 in complex with cu-CPT9C · the same entry in another collection · chain A against A, TM-score 1.00
Q9NR97 · AlphaFold monomer V2.0 prediction for toll-like receptor 8 (Q9NR97) · 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 Q9NR97
Elsewhere: RCSB PDB 5Z15 · PDBe 5Z15 · UniProt Q9NR97

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