7B6S

Sheep Polyomavirus VP1 in complex with 10 mM Forssman antigen pentaose

PDB DOI: https://doi.org/10.2210/pdb7B6S/pdb

Classification: VIRAL PROTEIN
Organism(s): Sheep polyomavirus 1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-12-08 Released: 2022-09-21
Deposition Author(s): Rustmeier, N.H., Stehle, T.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 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

DOI: https://doi.org/10.1101/2023.04.10.536218

Macromolecule Content

Total Structure Weight: 316.57 kDa
Atom Count: 23,447
Modelled Residue Count: 2,642
Deposited Residue Count: 2,760
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP1	A [auth AAA] B [auth BBB] C [auth CCC] D [auth DDD] E [auth EEE] A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD], E [auth EEE], F [auth FFF], G [auth GGG], H [auth HHH], I [auth III], J [auth JJJ]	276	Sheep polyomavirus 1	Mutation(s): 0
UniProt
Find proteins for A0A0E3ZCF3 (Sheep polyomavirus 1) Explore A0A0E3ZCF3 Go to UniProtKB: A0A0E3ZCF3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0E3ZCF3
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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]	4		N/A	Interactions Focus chain K [auth AaA] Focus chain L [auth BaB] Focus chain N [auth DaD] Focus chain P [auth FbF] Focus chain R [auth HaH] Focus chain S [auth IaI] Interactions & Density Focus chain K [auth AaA] Focus chain L [auth BaB] Focus chain N [auth DaD] Focus chain P [auth FbF] Focus chain R [auth HaH] Focus chain S [auth IaI]
Glycosylation Resources
GlyTouCan: G88796WA GlyCosmos: G88796WA

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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-glucopyranose	M [auth CaC], O [auth EaE], Q [auth GaG], T [auth JaJ]	5		N/A	Interactions Focus chain M [auth CaC] Focus chain O [auth EaE] Focus chain Q [auth GaG] Focus chain T [auth JaJ] Interactions & Density Focus chain M [auth CaC] Focus chain O [auth EaE] Focus chain Q [auth GaG] Focus chain T [auth JaJ]
Glycosylation Resources
GlyTouCan: G80062GG GlyCosmos: G80062GG GlyGen: G80062GG

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain IA [auth FFF] SDF format, chain NA [auth GGG] SDF format, chain WA [auth III] MOL2 format, chain IA [auth FFF] MOL2 format, chain NA [auth GGG] MOL2 format, chain WA [auth III]	IA [auth FFF], NA [auth GGG], WA [auth III]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain IA [auth FFF] Focus chain NA [auth GGG] Focus chain WA [auth III] Interactions & Density Focus chain IA [auth FFF] Focus chain NA [auth GGG] Focus chain WA [auth III]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain BA [auth DDD] SDF format, chain JA [auth FFF] SDF format, chain KA [auth FFF] SDF format, chain PA [auth HHH] SDF format, chain QA [auth HHH] SDF format, chain U [auth AAA] SDF format, chain W [auth BBB] SDF format, chain YA [auth JJJ] SDF format, chain UA [auth III] MOL2 format, chain BA [auth DDD] MOL2 format, chain JA [auth FFF] MOL2 format, chain KA [auth FFF] MOL2 format, chain PA [auth HHH] MOL2 format, chain QA [auth HHH] MOL2 format, chain U [auth AAA] MOL2 format, chain W [auth BBB] MOL2 format, chain YA [auth JJJ] MOL2 format, chain UA [auth III]	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		Interactions Focus chain BA [auth DDD] Focus chain JA [auth FFF] Focus chain KA [auth FFF] Focus chain PA [auth HHH] Focus chain QA [auth HHH] Focus chain U [auth AAA] Focus chain UA [auth III] Focus chain W [auth BBB] Focus chain YA [auth JJJ] Interactions & Density Focus chain BA [auth DDD] Focus chain JA [auth FFF] Focus chain KA [auth FFF] Focus chain PA [auth HHH] Focus chain QA [auth HHH] Focus chain U [auth AAA] Focus chain UA [auth III] Focus chain W [auth BBB] Focus chain YA [auth JJJ]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain GA [auth EEE] SDF format, chain MA [auth GGG] SDF format, chain RA [auth HHH] SDF format, chain VA [auth III] SDF format, chain Z [auth CCC] MOL2 format, chain GA [auth EEE] MOL2 format, chain MA [auth GGG] MOL2 format, chain RA [auth HHH] MOL2 format, chain VA [auth III] MOL2 format, chain Z [auth CCC]	GA [auth EEE], MA [auth GGG], RA [auth HHH], VA [auth III], Z [auth CCC]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain GA [auth EEE] Focus chain MA [auth GGG] Focus chain RA [auth HHH] Focus chain VA [auth III] Focus chain Z [auth CCC] Interactions & Density Focus chain GA [auth EEE] Focus chain MA [auth GGG] Focus chain RA [auth HHH] Focus chain VA [auth III] Focus chain Z [auth CCC]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain CA [auth DDD] SDF format, chain DA [auth DDD] SDF format, chain FA [auth EEE] SDF format, chain SA [auth HHH] SDF format, chain Y [auth CCC] SDF format, chain ZA [auth JJJ] MOL2 format, chain CA [auth DDD] MOL2 format, chain DA [auth DDD] MOL2 format, chain FA [auth EEE] MOL2 format, chain SA [auth HHH] MOL2 format, chain Y [auth CCC] MOL2 format, chain ZA [auth JJJ]	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		Interactions Focus chain CA [auth DDD] Focus chain DA [auth DDD] Focus chain FA [auth EEE] Focus chain SA [auth HHH] Focus chain Y [auth CCC] Focus chain ZA [auth JJJ] Interactions & Density Focus chain CA [auth DDD] Focus chain DA [auth DDD] Focus chain FA [auth EEE] Focus chain SA [auth HHH] Focus chain Y [auth CCC] Focus chain ZA [auth JJJ]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth CCC] SDF format, chain AB [auth JJJ] SDF format, chain EA [auth DDD] SDF format, chain LA [auth FFF] SDF format, chain OA [auth GGG] SDF format, chain TA [auth HHH] SDF format, chain V [auth AAA] SDF format, chain XA [auth III] SDF format, chain HA [auth EEE] SDF format, chain X [auth BBB] MOL2 format, chain AA [auth CCC] MOL2 format, chain AB [auth JJJ] MOL2 format, chain EA [auth DDD] MOL2 format, chain LA [auth FFF] MOL2 format, chain OA [auth GGG] MOL2 format, chain TA [auth HHH] MOL2 format, chain V [auth AAA] MOL2 format, chain XA [auth III] MOL2 format, chain HA [auth EEE] MOL2 format, chain X [auth BBB]	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		Interactions Focus chain AA [auth CCC] Focus chain AB [auth JJJ] Focus chain EA [auth DDD] Focus chain HA [auth EEE] Focus chain LA [auth FFF] Focus chain OA [auth GGG] Focus chain TA [auth HHH] Focus chain V [auth AAA] Focus chain X [auth BBB] Focus chain XA [auth III] Interactions & Density Focus chain AA [auth CCC] Focus chain AB [auth JJJ] Focus chain EA [auth DDD] Focus chain HA [auth EEE] Focus chain LA [auth FFF] Focus chain OA [auth GGG] Focus chain TA [auth HHH] Focus chain V [auth AAA] Focus chain X [auth BBB] Focus chain XA [auth III]