MolNFT v1 · #105278 · protein

Crystal structure of human TLR8 in complex with ORN06

4R07 · Toll-like receptor 8: “Crystal structure of human TLR8 in complex with ORN06”. X-ray diffraction, 5 ligands (URI, UCG, NAG), 20 pockets (best druggability 0.76). MolNFT v1 #105278 on GenesisL1: 3D structure, binding sites and…

PDB: 4R07
Type: protein
Length: 2,958 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Toll-like receptor 8
UniProt: Q9NR97
Ligands: URI, UCG, NAG, BMA, MAN
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 12% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Toll-like receptor 8	protein	747	12% helix, 15% strand	Q9NR97
B	Toll-like receptor 8	protein	738	11% helix, 15% strand	Q9NR97
C	Toll-like receptor 8	protein	738	12% helix, 15% strand	Q9NR97
D	Toll-like receptor 8	protein	735	12% helix, 15% strand	Q9NR97

Ligands and binding sites

URI · Uridine · ligand · 4 copies · chains A, B, C, D
UCG · 3'-O-[(R)-{[(2R,3aR,4R,6R,6aR)-6-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-2-hydroxy-2-oxidotetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-4-yl]methoxy}(hydroxy)phosphoryl]uridine 5'-(dihydrogen phosphate) · ligand · 4 copies · chains A, B, C, D
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 42 copies · chains A, B, C, D
BMA · beta-D-mannopyranose · sugar · 9 copies · chains A, B, C, D
MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	659	0.76	0.82	78	NAG, UCG
2	600	0.75	0.82	73	NAG, UCG
3	608	0.75	0.82	71	NAG, UCG
4	570	0.75	0.82	72	NAG, UCG
5	579	0.64	0.75	73	empty

Interfaces

3 interfaces between chains.

A–B · 2311 Å² buried · 37 hydrogen bonds · protein-protein
C–D · 2305 Å² buried · 37 hydrogen bonds · protein-protein
A–C · 255 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 30 glycan, 24 disulfide (N-glycosylation, disulfide).

Compared structures

4R07 · Crystal structure of human TLR8 in complex with ORN06 · the same entry in another collection · chain D against D, TM-score 1.00
Q9NR97 · AlphaFold monomer V2.0 prediction for toll-like receptor 8 (Q9NR97) · 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 Q9NR97
Elsewhere: RCSB PDB 4R07 · PDBe 4R07 · UniProt Q9NR97

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