5AZ5

Crystal structure of human TLR8 in complex with MB-343

PDB DOI: https://doi.org/10.2210/pdb5AZ5/pdb

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

Deposited: 2015-09-27 Released: 2016-10-05
Deposition Author(s): Tanji, H., Ohto, U., Shimizu, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.259
R-Value Work: 0.196
R-Value Observed: 0.199

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Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Crystal structure of human TLR8 in complex with MB-343

Tanji, H., Ohto, U., Shimizu, T.

To be published.

Macromolecule Content

Total Structure Weight: 382.39 kDa
Atom Count: 25,117
Modelled Residue Count: 2,991
Deposited Residue Count: 3,244
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 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, UNQ249/PRO286
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NR97
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, G, H	4		N-Glycosylation	Interactions Focus chain E Focus chain G Focus chain H Interactions & Density Focus chain E Focus chain G Focus chain H
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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

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

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M	4		N-Glycosylation	Interactions Focus chain M Interactions & Density Focus chain M
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MBL Query on MBL Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain Q [auth A] SDF format, chain U [auth A] SDF format, chain Z [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain U [auth A] MOL2 format, chain Z [auth C]	EA [auth C], Q [auth A], U [auth A], Z [auth C]	1-pentyl-4-phenyl-imidazol-2-amine C₁₄ H₁₉ N₃ NTJHSIKKNQRLPN-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain Q [auth A] Focus chain U [auth A] Focus chain Z [auth C] Interactions & Density Focus chain EA [auth C] Focus chain Q [auth A] Focus chain U [auth A] Focus chain Z [auth C]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain HA [auth D] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain AA [auth C]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] FA [auth D] AA [auth C], BA [auth C], CA [auth C], DA [auth C], FA [auth D], GA [auth D], HA [auth D], R [auth A], S [auth A], T [auth A], V [auth B], W [auth B], X [auth B], Y [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.259
R-Value Work: 0.196
R-Value Observed: 0.199
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.627	α = 90
b = 141.119	β = 90.32
c = 170.972	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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Entry History

Deposition Data

Released Date: 2016-10-05

Deposition Author(s):

Tanji, H.

Ohto, U.

Shimizu, T.

Revision History (Full details and data files)

Version 1.0: 2016-10-05
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

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Help and Resources

5AZ5

Crystal structure of human TLR8 in complex with MB-343

Crystal structure of human TLR8 in complex with MB-343

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Entity ID: 3

Glycosylation Resources

Entity ID: 4

Glycosylation Resources

Entity ID: 5

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)