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 
• Deposition Author(s): Neu, U., Stehle, T.

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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 

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 152.04 kDa 
• Atom Count: 11,292 
• Modelled Residue Count: 1,318 
• Deposited Residue Count: 1,360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP1	A, B, C, D, E	272	Betapolyomavirus macacae	Mutation(s): 0  Gene Names: VP1
UniProt
Find proteins for P03087 (Simian virus 40) Explore P03087  Go to UniProtKB:  P03087

Oligosaccharides

Help

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
EDO	I [auth A], J [auth A], K [auth B], L [auth C], M [auth D], N [auth E]	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 Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-04 
Deposition Author(s): Neu, U., Stehle, T.

Revision History  

• 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