3BWR
SV40 VP1 pentamer in complex with GM1 oligosaccharide
- PDB DOI: https://doi.org/10.2210/pdb3BWR/pdb
- Classification: VIRAL PROTEIN
- Organism(s): Betapolyomavirus macacae
- Expression System: Escherichia coli
- Mutation(s): No 
- Deposited: 2008-01-10 Released: 2008-03-04 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.25 Å
- R-Value Free: 0.233 
- R-Value Work: 0.187 
- R-Value Observed: 0.192 
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 |
Capsid protein VP1 | 272 | Betapolyomavirus macacae | Mutation(s): 0  Gene Names: VP1 | ||
UniProt | |||||
Find proteins for P03087 (Simian virus 40) Explore P03087  Go to UniProtKB:  P03087 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P03087 | ||||
Sequence AnnotationsExpand | |||||
|
Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose | F, G, H | 5 | N/A | ||
Glycosylation Resources | |||||
GlyTouCan:  G48558GR GlyCosmos:  G48558GR GlyGen:  G48558GR |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
EDO Query on EDO | I [auth A] J [auth A] K [auth B] L [auth C] M [auth D] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.25 Å
- R-Value Free: 0.233 
- R-Value Work: 0.187 
- R-Value Observed: 0.192 
- Space Group: C 1 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 152.764 | α = 90 |
b = 93.087 | β = 105.6 |
c = 118.882 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |
Entry History 
Deposition Data
- Released Date: 2008-03-04  Deposition Author(s): Neu, U., Stehle, T.
Revision History (Full details and data files)
- Version 1.0: 2008-03-04
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2011-10-05
Changes: Other - Version 1.3: 2017-10-25
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: 2023-08-30
Changes: Data collection, Database references, Refinement description, Structure summary