MolNFT v1 · #113915 · protein

Crystal structure of human TLR8 in complex with mb-564

5AWC · Toll-like receptor 8: “Crystal structure of human TLR8 in complex with mb-564”. X-ray diffraction, 3 ligands (M4D, NAG, BMA), 20 pockets (best druggability 0.76). MolNFT v1 #113915 on GenesisL1: 3D structure, binding sites and…

PDB: 5AWC
Type: protein
Length: 2,942 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Toll-like receptor 8
UniProt: Q9NR97
Ligands: M4D, NAG, BMA
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 11% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Toll-like receptor 8	protein	749	13% helix, 15% strand	Q9NR97
B	Toll-like receptor 8	protein	742	11% helix, 15% strand	Q9NR97
C	Toll-like receptor 8	protein	727	12% helix, 15% strand	Q9NR97
D	Toll-like receptor 8	protein	724	10% helix, 14% strand	Q9NR97

Ligands and binding sites

M4D · 5-(4-azanylbutyl)-3-pentyl-quinolin-2-amine · ligand · 4 copies · chains A, B, C, D
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 33 copies · chains A, B, C, D
BMA · beta-D-mannopyranose · sugar · 8 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1177	0.76	0.79	105	NAG
2	884	0.76	0.79	84	NAG
3	856	0.75	0.79	88	NAG
4	785	0.75	0.80	86	NAG
5	268	0.61	0.79	27	M4D

Interfaces

3 interfaces between chains.

A–B · 2164 Å² buried · 31 hydrogen bonds · protein-protein
C–D · 2146 Å² buried · 32 hydrogen bonds · protein-protein
A–C · 538 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 disulfide, 21 glycan (disulfide, N-glycosylation).

Compared structures

5AWC · Crystal structure of human TLR8 in complex with MB-564 · 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 5AWC · PDBe 5AWC · UniProt Q9NR97

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