4JCF
S268F Variant of JC Polyomavirus Major Capsid Protein VP1 in Complex with LSTc
- PDB DOI: https://doi.org/10.2210/pdb4JCF/pdb
- Classification: VIRAL PROTEIN
- Organism(s): JC polyomavirus
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes 
- Deposited: 2013-02-21 Released: 2013-08-14 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.201 
- R-Value Work: 0.164 
- R-Value Observed: 0.166 
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 |
Major capsid protein VP1 | A [auth C], B [auth A], C [auth B], D, E | 272 | JC polyomavirus | Mutation(s): 1  | |
UniProt | |||||
Find proteins for P03089 (JC polyomavirus) Explore P03089  Go to UniProtKB:  P03089 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P03089 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
GOL Query on GOL | G [auth C], H [auth A], J [auth B], K [auth D], L [auth E] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
EDO Query on EDO | I [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2 | |||||
---|---|---|---|---|---|
ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_900046 Query on PRD_900046 | F | 6'-sialyl-N-acetyllactosamine | Oligosaccharide / Glycan component |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.201 
- R-Value Work: 0.164 
- R-Value Observed: 0.166 
- Space Group: C 1 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 149.97 | α = 90 |
b = 96.06 | β = 110.36 |
c = 128.22 | γ = 90 |
Software Name | Purpose |
---|---|
RemDAq | data collection |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
Entry History 
Deposition Data
- Released Date: 2013-08-14  Deposition Author(s): Stehle, T., Stroh, L.J.
Revision History (Full details and data files)
- Version 1.0: 2013-08-14
Type: Initial release - Version 1.1: 2017-11-15
Changes: Refinement description - 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: 2023-09-20
Changes: Data collection, Database references, Refinement description, Structure summary