7B6V

Sheep Polyomavirus VP1 in complex with 5 mM Forssman antigen pentaose and 20 mM 3'-sialyllactosamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.152 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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

Help

Entity ID: 2
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
K [auth AaA],
L [auth BaB],
N [auth DaD],
O [auth EaE],
P [auth FaF],
K [auth AaA],
L [auth BaB],
N [auth DaD],
O [auth EaE],
P [auth FaF],
Q [auth GaG],
R [auth HaH],
S [auth IaI],
T [auth JaJ]
4N/A
Glycosylation Resources
GlyTouCan:  G88796WA
GlyCosmos:  G88796WA
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-(1-4)-beta-D-glucopyranoseM [auth CaC]5N/A
Glycosylation Resources
GlyTouCan:  G80062GG
GlyCosmos:  G80062GG
GlyGen:  G80062GG
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SIA (Subject of Investigation/LOI)
Query on SIA

Download Ideal Coordinates CCD File 
DA [auth FFF],
GA [auth HHH],
JA [auth III],
U [auth AAA],
Y [auth DDD]
N-acetyl-alpha-neuraminic acid
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
PGE
Query on PGE

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LA [auth JJJ]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

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MA [auth JJJ]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

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AA [auth EEE],
BA [auth EEE],
HA [auth HHH]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
CA [auth EEE]
EA [auth FFF]
FA [auth GGG]
IA [auth HHH]
KA [auth III]
CA [auth EEE],
EA [auth FFF],
FA [auth GGG],
IA [auth HHH],
KA [auth III],
NA [auth JJJ],
V [auth AAA],
W [auth BBB],
X [auth CCC],
Z [auth DDD]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.152 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.404α = 90
b = 130.404β = 90
c = 221.221γ = 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