3TB0
Crystal structure of Rhesus Rotavirus VP8* in complex with N-Glycolylneuraminic acid
- PDB DOI: https://doi.org/10.2210/pdb3TB0/pdb
- Classification: SUGAR BINDING PROTEIN, VIRAL PROTEIN
- Organism(s): Simian rotavirus A strain RRV
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2011-08-04 Released: 2012-10-17
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.249
- R-Value Work: 0.183
- R-Value Observed: 0.186
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 |
| Outer capsid protein VP4 | 161 | Simian rotavirus A strain RRV | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for P12473 (Rotavirus A (strain RVA/Monkey/United States/RRV/1975/G3P5B[3])) Explore P12473 Go to UniProtKB: P12473 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P12473 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MN0 Query on MN0 | B [auth A] | methyl 3,5-dideoxy-5-[(hydroxyacetyl)amino]-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid C12 H21 N O10 NFUCYHODBBSMAK-BLMTXZDNSA-N |  | ||
| 1PE Query on 1PE | E [auth A] | PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N |  | ||
| GOL Query on GOL | C [auth A], D [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.249
- R-Value Work: 0.183
- R-Value Observed: 0.186
- Space Group: P 41 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 48.42 | α = 90 |
| b = 48.42 | β = 90 |
| c = 130.91 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
Entry History
Deposition Data
- Released Date: 2012-10-17 Deposition Author(s): Yu, X., Blanchard, H.
Revision History (Full details and data files)
- Version 1.0: 2012-10-17
Type: Initial release - Version 1.1: 2012-12-05
Changes: Database references - Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations - Version 1.3: 2024-02-28
Changes: Data collection, Database references, Structure summary
