7B6U

Sheep Polyomavirus VP1 in complex with 5 mM Forssman antigen pentaose and 20 mM 6'-sialyllactosamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.146 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

A novel and highly specific Forssman antigen-binding protein from sheep polyomavirus

Rustmeier, N.H.Silva, L.M.Di Maio, A.Mueller, J.C.Herrmann, A.Feizi, T.Liu, Y.Stehle, T.

(2023) bioRxiv 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence 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
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseK [auth AaA],
O [auth DaD],
R [auth FaF],
U [auth HaH],
X [auth JaJ]
3N/A
Glycosylation Resources
GlyTouCan:  G73578JC
GlyCosmos:  G73578JC
GlyGen:  G73578JC
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D 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
L [auth AdA],
M [auth BbB],
N [auth CaC],
P [auth DdD],
Q [auth EaE],
L [auth AdA],
M [auth BbB],
N [auth CaC],
P [auth DdD],
Q [auth EaE],
S [auth FdF],
T [auth GaG],
V [auth HdH],
W [auth IaI],
Y [auth JdJ]
4N/A
Glycosylation Resources
GlyTouCan:  G88796WA
GlyCosmos:  G88796WA
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SIA (Subject of Investigation/LOI)
Query on SIA

Download Ideal Coordinates CCD File 
BA [auth BBB]N-acetyl-alpha-neuraminic acid
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
PGE
Query on PGE

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LA [auth GGG],
OA [auth HHH]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
AA [auth AAA]
CA [auth BBB]
EA [auth BBB]
FA [auth CCC]
GA [auth DDD]
AA [auth AAA],
CA [auth BBB],
EA [auth BBB],
FA [auth CCC],
GA [auth DDD],
IA [auth EEE],
JA [auth FFF],
NA [auth GGG],
PA [auth HHH],
QA [auth HHH],
SA [auth III],
UA [auth JJJ]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
DA [auth BBB]
HA [auth EEE]
KA [auth FFF]
MA [auth GGG]
RA [auth III]
DA [auth BBB],
HA [auth EEE],
KA [auth FFF],
MA [auth GGG],
RA [auth III],
TA [auth III],
Z [auth AAA]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.146 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.645α = 90
b = 129.645β = 90
c = 220.431γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


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
  • Version 1.1: 2022-10-05
    Changes: Derived calculations
  • Version 1.2: 2023-04-19
    Changes: Database references
  • Version 1.3: 2024-02-07
    Changes: Data collection, Refinement description