1KQR
Crystal Structure of the Rhesus Rotavirus VP4 Sialic Acid Binding Domain in Complex with 2-O-methyl-alpha-D-N-acetyl neuraminic acid
- PDB DOI: https://doi.org/10.2210/pdb1KQR/pdb
- BMRB: 5275
- Classification: VIRAL PROTEIN
- Organism(s): Simian rotavirus A strain RRV
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2002-01-07 Released: 2002-03-27
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.40 Å
- R-Value Free: 0.181
- R-Value Work: 0.169
This is version 1.4 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 |
| VP4 | 179 | Simian rotavirus A strain RRV | Mutation(s): 0 Gene Names: segment 4 |  | |
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 | |
| MNA Query on MNA | C [auth A] | 2-O-methyl-5-N-acetyl-alpha-D-neuraminic acid C12 H21 N O9 NJRVVFURCKKXOD-MIDKXNQYSA-N |  | ||
| SO4 Query on SO4 | B [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| GOL Query on GOL | D [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.40 Å
- R-Value Free: 0.181
- R-Value Work: 0.169
- Space Group: P 41 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 48.027 | α = 90 |
| b = 48.027 | β = 90 |
| c = 130.404 | γ = 90 |
| Software Name | Purpose |
|---|---|
| CNS | refinement |
| DENZO | data reduction |
| HKL-2000 | data scaling |
| CNS | phasing |
Entry History
Deposition Data
- Released Date: 2002-03-27 Deposition Author(s): Dormitzer, P.R., Sun, Z.-Y.J., Wagner, G., Harrison, S.C.
Revision History (Full details and data files)
- Version 1.0: 2002-03-27
Type: Initial release - Version 1.1: 2008-04-27
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary - Version 1.4: 2024-02-14
Changes: Data collection, Database references, Structure summary
