6LFJ
Crystal structure of mouse DCAR2 CRD domain complex with IPM2
- PDB DOI: https://doi.org/10.2210/pdb6LFJ/pdb
- Classification: SUGAR BINDING PROTEIN
- Organism(s): Mus musculus
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2019-12-03 Released: 2020-03-25
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.84 Å
- R-Value Free: 0.198
- R-Value Work: 0.177
- R-Value Observed: 0.178
This is version 1.3 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 |
| C-type lectin domain family 4, member b1 | 136 | Mus musculus | Mutation(s): 0 Gene Names: Clec4b1, Clec4b, Dcar |  | |
UniProt | |||||
Find proteins for Q9D8Q7 (Mus musculus) Explore Q9D8Q7 Go to UniProtKB: Q9D8Q7 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9D8Q7 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| B3P Query on B3P | D [auth A] | 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C11 H26 N2 O6 HHKZCCWKTZRCCL-UHFFFAOYSA-N |  | ||
| IPD Query on IPD | F [auth A], I [auth B] | D-MYO-INOSITOL-1-PHOSPHATE C6 H11 O9 P INAPMGSXUVUWAF-UOTPTPDRSA-L |  | ||
| MAN Query on MAN | E [auth A], G [auth A], J [auth B] | alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N |  | ||
| CA Query on CA | C [auth A], H [auth B] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.84 Å
- R-Value Free: 0.198
- R-Value Work: 0.177
- R-Value Observed: 0.178
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 65.689 | α = 90 |
| b = 72.564 | β = 90 |
| c = 100.469 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| XDS | data scaling |
| MOLREP | phasing |
Entry History
Deposition Data
- Released Date: 2020-03-25 Deposition Author(s): Omahdi, Z., Horikawa, Y., Toyonaga, K., Kakuta, Y., Yamasaki, S.
Revision History (Full details and data files)
- Version 1.0: 2020-03-25
Type: Initial release - Version 1.1: 2020-05-06
Changes: Database references - Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.3: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
