3WPH
Crystal structure of mouse TLR9 in complex with inhibitory DNA4084 (form 2)
- PDB DOI: https://doi.org/10.2210/pdb3WPH/pdb
- NAKB: 3WPH
- 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: 2.33 Å
- R-Value Free: 0.247
- R-Value Work: 0.213
- R-Value Observed: 0.215
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 | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | C [auth A], D [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| SO4 Query on SO4 | E [auth A], F [auth A], G [auth B] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.33 Å
- R-Value Free: 0.247
- R-Value Work: 0.213
- R-Value Observed: 0.215
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 136.41 | α = 90 |
| b = 130.1 | β = 91.54 |
| c = 71.33 | 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
