5AWC | pdb_00005awc

Crystal structure of human TLR8 in complex with MB-564

PDB DOI: https://doi.org/10.2210/pdb5AWC/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Drosophila
Mutation(s): No

Deposited: 2015-07-03 Released: 2016-07-20
Deposition Author(s): Tanji, H., Ohto, U., Shimizu, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.269 (Depositor), 0.267 (DCC)
R-Value Work:
0.209 (Depositor), 0.212 (DCC)
R-Value Observed:
0.212 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Structure-based Design of Human TLR8-specific Agonists with Augmented Potency and Adjuvanticity

Beesu, M., Caruso, G., Salyer, A.C.D., Khetani, K.K., Sil, D., Weerasinghe, M., Tanji, H., Ohto, U., Shimizu, T., David, S.A.

To be published.

Macromolecule Content

Total Structure Weight: 380.86 kDa
Atom Count: 24,478
Modeled Residue Count: 2,942
Deposited Residue Count: 3,244
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toll-like receptor 8	A, B, C, D	811	Homo sapiens	Mutation(s): 0 Gene Names: TLR8
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NR97 (Homo sapiens) Explore Q9NR97 Go to UniProtKB: Q9NR97
PHAROS: Q9NR97 GTEx: ENSG00000101916
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NR97
Glycosylation
Glycosylation Sites: 5	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D	Go to GlyGen: Q9NR97-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, G, H, J, K E, G, H, J, K, M, N, P	3		N-Glycosylation	Interactions Focus chain E Focus chain G Focus chain H Focus chain J Focus chain K Focus chain M Focus chain N Focus chain P Interactions & Density Focus chain E Focus chain G Focus chain H Focus chain J Focus chain K Focus chain M Focus chain N Focus chain P
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, I, L, O	2		N-Glycosylation	Interactions Focus chain F Focus chain I Focus chain L Focus chain O Interactions & Density Focus chain F Focus chain I Focus chain L Focus chain O
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
M4D Query on M4D Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain U [auth B] SDF format, chain T [auth A] SDF format, chain AA [auth D] MOL2 format, chain Z [auth C] MOL2 format, chain U [auth B] MOL2 format, chain T [auth A] MOL2 format, chain AA [auth D] mmCIF format, chain Z [auth C] mmCIF format, chain U [auth B] mmCIF format, chain T [auth A] mmCIF format, chain AA [auth D]	AA [auth D], T [auth A], U [auth B], Z [auth C]	5-(4-azanylbutyl)-3-pentyl-quinolin-2-amine C₁₈ H₂₇ N₃ GHXJTPWIBLPAON-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain T [auth A] Focus chain U [auth B] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth D] Focus chain T [auth A] Focus chain U [auth B] Focus chain Z [auth C]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain X [auth C] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain CA [auth D] SDF format, chain BA [auth D] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain CA [auth D] MOL2 format, chain BA [auth D] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth C] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain CA [auth D] mmCIF format, chain BA [auth D]	BA [auth D] CA [auth D] Q [auth A] R [auth A] S [auth A] BA [auth D], CA [auth D], Q [auth A], R [auth A], S [auth A], V [auth B], W [auth B], X [auth C], Y [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth C] Focus chain Y [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
M4D	BindingDB: 5AWC	EC50: 27 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.269 (Depositor), 0.267 (DCC)
R-Value Work: 0.209 (Depositor), 0.212 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.401	α = 90
b = 140.175	β = 90.47
c = 169.603	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-07-20

Deposition Author(s):

Tanji, H.

Ohto, U.

Shimizu, T.

Revision History (Full details and data files)

Version 1.0: 2016-07-20
Type: Initial release
Version 1.1: 2017-10-04
Changes: Data collection, Derived calculations
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-10-16
Changes: Data collection, Database references, Structure summary