Download MendeleyCrystal structure of Dioclea violacea seed lectin
Gallego del Sol, F., Chornet, J.J.C., Cavada, B.S.To be published.
2GDF
Crystal structure of Dioclea violacea seed lectin
- PDB DOI: https://doi.org/10.2210/pdb2GDF/pdb
- Classification: SUGAR BINDING PROTEIN
- Organism(s): Macropsychanthus violaceus
- Mutation(s): No
- Deposited: 2006-03-16 Released: 2006-09-16
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.258
- R-Value Work: 0.227
- R-Value Observed: 0.228
wwPDB Validation 3D Report Full Report
This is version 1.3 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| lectin | 237 | Macropsychanthus violaceus | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for P08902 (Dioclea grandiflora) Explore P08902 Go to UniProtKB: P08902 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P08902 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MN Query on MN | E [auth B], G [auth D] | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N |  | ||
| CA Query on CA | F [auth B], H [auth D] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.258
- R-Value Work: 0.227
- R-Value Observed: 0.228
- Space Group: P 32
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 72.938 | α = 90 |
| b = 72.938 | β = 90 |
| c = 161.362 | γ = 120 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| MOSFLM | data reduction |
| CCP4 | data scaling |
| AMoRE | phasing |
Entry History
Deposition Data
- Released Date: 2006-09-16 Deposition Author(s): Gallego del Sol, F., Chornet, J.J.C., Cavada, B.S.
Revision History (Full details and data files)
- Version 1.0: 2006-09-16
Type: Initial release - Version 1.1: 2008-05-01
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Version format compliance - Version 1.3: 2024-03-13
Changes: Data collection, Database references, Derived calculations
