7B6S

Sheep Polyomavirus VP1 in complex with 10 mM Forssman antigen pentaose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.149 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

The Non-Sialylated Forssman Glycan Serves as a Ligand for Sheep Polyomavirus

Rustmeier, N.H.Liu, Y.Herrmann, A.Feizi, T.Stehle, T.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Capsid protein VP1276Sheep polyomavirus 1Mutation(s): 0 
UniProt
Find proteins for A0A0E3ZCF3 (Sheep polyomavirus 1)
Explore A0A0E3ZCF3 
Go to UniProtKB:  A0A0E3ZCF3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0E3ZCF3
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose
K [auth AaA],
L [auth BaB],
N [auth DaD],
P [auth FbF],
R [auth HaH],
K [auth AaA],
L [auth BaB],
N [auth DaD],
P [auth FbF],
R [auth HaH],
S [auth IaI]
4N/A Oligosaccharides Interaction
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranoseM [auth CaC],
O [auth EaE],
Q [auth GaG],
T [auth JaJ]
5N/A Oligosaccharides Interaction
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download Ideal Coordinates CCD File 
IA [auth FFF],
NA [auth GGG],
WA [auth III]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
BA [auth DDD],
JA [auth FFF],
KA [auth FFF],
PA [auth HHH],
QA [auth HHH],
BA [auth DDD],
JA [auth FFF],
KA [auth FFF],
PA [auth HHH],
QA [auth HHH],
U [auth AAA],
UA [auth III],
W [auth BBB],
YA [auth JJJ]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
GA [auth EEE],
MA [auth GGG],
RA [auth HHH],
VA [auth III],
Z [auth CCC]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
CA [auth DDD],
DA [auth DDD],
FA [auth EEE],
SA [auth HHH],
Y [auth CCC],
CA [auth DDD],
DA [auth DDD],
FA [auth EEE],
SA [auth HHH],
Y [auth CCC],
ZA [auth JJJ]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth CCC],
AB [auth JJJ],
EA [auth DDD],
HA [auth EEE],
LA [auth FFF],
AA [auth CCC],
AB [auth JJJ],
EA [auth DDD],
HA [auth EEE],
LA [auth FFF],
OA [auth GGG],
TA [auth HHH],
V [auth AAA],
X [auth BBB],
XA [auth III]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.149 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.494α = 90
b = 130.494β = 90
c = 222.435γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyFOR2327

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-21
    Type: Initial release