3SIT
Crystal structure of porcine CRW-8 Rotavirus VP8* in complex with aceramido-GM3
- PDB DOI: https://doi.org/10.2210/pdb3SIT/pdb
- Classification: SUGAR BINDING PROTEIN, VIRAL PROTEIN
- Organism(s): Porcine rotavirus (serotype 3 / strain CRW-8)
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes
- Deposited: 2011-06-20 Released: 2011-09-28
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.213
- R-Value Work: 0.184
- R-Value Observed: 0.185
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 |
| Outer capsid protein VP4 | 163 | Porcine rotavirus (serotype 3 / strain CRW-8) | Mutation(s): 4 |  | |
UniProt | |||||
Find proteins for P0C6Y8 (Rotavirus A (isolate RVA/Pig/Australia/CRW-8/1987/G3P9[7])) Explore P0C6Y8 Go to UniProtKB: P0C6Y8 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P0C6Y8 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MRD Query on MRD | F [auth A], H [auth B] | (4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N |  | ||
| NA Query on NA | E [auth A], G [auth B] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_900025 Query on PRD_900025 | C, D | 3'-sialyl-alpha-lactose | Oligosaccharide / Nutrient |  | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.213
- R-Value Work: 0.184
- R-Value Observed: 0.185
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 56.777 | α = 90 |
| b = 57.357 | β = 90 |
| c = 113.129 | γ = 90 |
| Software Name | Purpose |
|---|---|
| Blu-Ice | data collection |
| AMoRE | phasing |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
Entry History
Deposition Data
- Released Date: 2011-09-28 Deposition Author(s): Blanchard, H., Yu, X.
Revision History (Full details and data files)
- Version 1.0: 2011-09-28
Type: Initial release - Version 1.1: 2011-10-12
Changes: Database references - Version 1.2: 2011-11-30
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary - Version 2.1: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary
