6A7S
Ca2+-independent C-type lectin SPL-2 from Saxidomus purpuratus
- PDB DOI: https://doi.org/10.2210/pdb6A7S/pdb
- Classification: SUGAR BINDING PROTEIN
- Organism(s): Saxidomus purpurata
- Mutation(s): No
- Deposited: 2018-07-04 Released: 2019-03-20
- Funding Organization(s): Japan Society for the Promotion of Science
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.207
- R-Value Work: 0.179
- R-Value Observed: 0.181
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 |
| N-acetylglucosamine-specific lectin | A [auth B] | 159 | Saxidomus purpurata | Mutation(s): 0 |  |
UniProt | |||||
Find proteins for A0A2Z6G7U3 (Saxidomus purpurata) Explore A0A2Z6G7U3 Go to UniProtKB: A0A2Z6G7U3 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A2Z6G7U3 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NGA Query on NGA | B | 2-acetamido-2-deoxy-beta-D-galactopyranose C8 H15 N O6 OVRNDRQMDRJTHS-JAJWTYFOSA-N |  | ||
| TRS Query on TRS | C [auth B] | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O |  | ||
| SO4 Query on SO4 | E [auth B] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| CA Query on CA | D [auth B] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.207
- R-Value Work: 0.179
- R-Value Observed: 0.181
- Space Group: P 31 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 91.235 | α = 90 |
| b = 91.235 | β = 90 |
| c = 48.791 | γ = 120 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| MOLREP | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2019-03-20 Deposition Author(s): Unno, H., Hatakeyama, T.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Japan Society for the Promotion of Science | Japan | 25450133 |
| Japan Society for the Promotion of Science | Japan | 17K07760 |
| Japan Society for the Promotion of Science | Japan | 26450128 |
| Japan Society for the Promotion of Science | Japan | 15K06977 |
Revision History (Full details and data files)
- Version 1.0: 2019-03-20
Type: Initial release - Version 1.1: 2019-04-03
Changes: Data collection, Database references, Structure summary - Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
