5KOV
Crystal structure of the human astrovirus 2 capsid protein spike in complex with a single chain variable fragment of an astrovirus neutralizing antibody at 3.24-A resolution
- PDB DOI: https://doi.org/10.2210/pdb5KOV/pdb
- Classification: VIRAL PROTEIN
- Organism(s): Human astrovirus 2, Mus musculus
- Expression System: Escherichia coli BL21(DE3), Drosophila melanogaster
- Mutation(s): No 
- Deposited: 2016-07-01 Released: 2016-11-09 
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.25 Å
- R-Value Free: 0.288 
- R-Value Work: 0.241 
- R-Value Observed: 0.243 
This is version 1.7 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 |
Capsid polyprotein VP90 | 228 | Human astrovirus 2 | Mutation(s): 0  Gene Names: ORF2 | ||
UniProt | |||||
Find proteins for Q82446 (Human astrovirus-2) Explore Q82446  Go to UniProtKB:  Q82446 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q82446 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
PL-2 scFv chain | 251 | Mus musculus | Mutation(s): 0  | ||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | Q [auth C], R [auth E], S [auth K], T [auth I] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.25 Å
- R-Value Free: 0.288 
- R-Value Work: 0.241 
- R-Value Observed: 0.243 
- Space Group: P 41
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 199.998 | α = 90 |
b = 199.998 | β = 90 |
c = 157.515 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
HKL-2000 | data collection |
HKL-2000 | data scaling |
PHASER | phasing |
PDB_EXTRACT | data extraction |
Coot | model building |
HKL-2000 | data reduction |
Entry History & Funding Information
Deposition Data
- Released Date: 2016-11-09  Deposition Author(s): Bogdanoff, W.A., DuBois, R.M.
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | AI095369 |
Revision History (Full details and data files)
- Version 1.0: 2016-11-09
Type: Initial release - Version 1.1: 2016-11-16
Changes: Database references - Version 1.2: 2017-01-18
Changes: Database references - Version 1.3: 2017-09-06
Changes: Author supporting evidence - Version 1.4: 2017-11-01
Changes: Author supporting evidence - Version 1.5: 2019-12-11
Changes: Author supporting evidence - Version 1.6: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.7: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary