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 
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 
This is version 2.0 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Toll-like receptor 8 | 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 AnnotationsExpand | |||||
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Oligosaccharides
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 | ||
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 | ||
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 | ||
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 | ||
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 | 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 | |||
NAG Query on NAG | AA [auth C] BA [auth C] CA [auth C] DA [auth C] FA [auth D] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
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 Name | Purpose |
---|---|
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
MOLREP | phasing |
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