2VMC
Structure of the complex of discoidin II from Dictyostelium discoideum with N-acetyl-galactosamine
- PDB DOI: https://doi.org/10.2210/pdb2VMC/pdb
- Classification: CELL ADHESION
- Organism(s): Dictyostelium discoideum AX2
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2008-01-25 Released: 2008-07-01
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.198
- R-Value Work: 0.157
- R-Value Observed: 0.159
wwPDB Validation 3D Report Full Report
This is version 2.1 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 |
| DISCOIDIN-2 | 257 | Dictyostelium discoideum AX2 | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for P42530 (Dictyostelium discoideum) Explore P42530 Go to UniProtKB: P42530 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P42530 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 6 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 1PG Query on 1PG | G [auth A], H [auth A] | 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL C11 H24 O6 SLNYBUIEAMRFSZ-UHFFFAOYSA-N |  | ||
| NGA Query on NGA | F [auth A] | 2-acetamido-2-deoxy-beta-D-galactopyranose C8 H15 N O6 OVRNDRQMDRJTHS-JAJWTYFOSA-N |  | ||
| A2G Query on A2G | E [auth A] | 2-acetamido-2-deoxy-alpha-D-galactopyranose C8 H15 N O6 OVRNDRQMDRJTHS-CBQIKETKSA-N |  | ||
| EDO Query on EDO | I [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| CA Query on CA | D [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
| CL Query on CL | B [auth A], C [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.198
- R-Value Work: 0.157
- R-Value Observed: 0.159
- Space Group: H 3 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 82.52 | α = 90 |
| b = 82.52 | β = 90 |
| c = 261.6 | γ = 120 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| XDS | data reduction |
| SCALA | data scaling |
| AMoRE | phasing |
Entry History
Deposition Data
- Released Date: 2008-07-01 Deposition Author(s): Saboia, K., Satre, M., Imberty, A., Varrot, A.
Revision History (Full details and data files)
- Version 1.0: 2008-07-01
Type: Initial release - Version 1.1: 2011-06-02
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary - Version 2.1: 2023-12-13
Changes: Data collection, Database references, Refinement description, Structure summary
