3WPG
Crystal structure of mouse TLR9 in complex with inhibitory DNA4084 (form 1)
- PDB DOI: https://doi.org/10.2210/pdb3WPG/pdb
- NAKB: 3WPG
- Classification: DNA BINDING PROTEIN/DNA
- Organism(s): Mus musculus, synthetic construct
- Expression System: Drosophila melanogaster
- Mutation(s): Yes 
- Deposited: 2014-01-11 Released: 2015-02-11 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.25 Å
- R-Value Free: 0.280 
- R-Value Work: 0.236 
- R-Value Observed: 0.238 
This is version 1.2 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 9 | 803 | Mus musculus | Mutation(s): 7  Gene Names: Tlr9 | ||
UniProt | |||||
Find proteins for Q9EQU3 (Mus musculus) Explore Q9EQU3  Go to UniProtKB:  Q9EQU3 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9EQU3 | ||||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | Organism | Image | |
DNA (5'-D(*CP*CP*TP*GP*GP*AP*TP*GP*GP*GP*AP*A)-3') | 12 | synthetic construct | |||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | C [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
SO4 Query on SO4 | D [auth A], E [auth A], F [auth A], G [auth A], H [auth B] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.25 Å
- R-Value Free: 0.280 
- R-Value Work: 0.236 
- R-Value Observed: 0.238 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 71.23 | α = 90 |
b = 123.86 | β = 90 |
c = 130.44 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
PDB_EXTRACT | data extraction |
MOSFLM | data reduction |
SCALA | data scaling |
MOLREP | phasing |
Entry History 
Deposition Data
- Released Date: 2015-02-11  Deposition Author(s): Ohto, U., Shimizu, T.
Revision History (Full details and data files)
- Version 1.0: 2015-02-11
Type: Initial release - Version 1.1: 2015-05-06
Changes: Database references - Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary