7B6V | pdb_00007b6v

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

PDB DOI: https://doi.org/10.2210/pdb7B6V/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: 1.80 Å
R-Value Free:
0.177 (Depositor), 0.180 (DCC)
R-Value Work:
0.152 (Depositor), 0.160 (DCC)

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

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

Macromolecule Content

Total Structure Weight: 315.66 kDa
Atom Count: 23,360
Modeled Residue Count: 2,633
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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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], 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]	4		N/A	Interactions Focus chain K [auth AaA] Focus chain L [auth BaB] Focus chain N [auth DaD] Focus chain O [auth EaE] Focus chain P [auth FaF] Focus chain Q [auth GaG] Focus chain R [auth HaH] Focus chain S [auth IaI] Focus chain T [auth JaJ] Interactions & Density Focus chain K [auth AaA] Focus chain L [auth BaB] Focus chain N [auth DaD] Focus chain O [auth EaE] Focus chain P [auth FaF] Focus chain Q [auth GaG] Focus chain R [auth HaH] Focus chain S [auth IaI] Focus chain T [auth JaJ]
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]	5		N/A	Interactions Focus chain M [auth CaC] Interactions & Density Focus chain M [auth CaC]
Glycosylation Resources
GlyTouCan: G80062GG GlyCosmos: G80062GG GlyGen: G80062GG

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SIA (Subject of Investigation/LOI) Query on SIA Download Ideal Coordinates CCD File SDF format, chain DA [auth FFF] SDF format, chain GA [auth HHH] SDF format, chain JA [auth III] SDF format, chain U [auth AAA] SDF format, chain Y [auth DDD] MOL2 format, chain DA [auth FFF] MOL2 format, chain GA [auth HHH] MOL2 format, chain JA [auth III] MOL2 format, chain U [auth AAA] MOL2 format, chain Y [auth DDD] mmCIF format, chain DA [auth FFF] mmCIF format, chain GA [auth HHH] mmCIF format, chain JA [auth III] mmCIF format, chain U [auth AAA] mmCIF format, chain Y [auth DDD]	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		Interactions Focus chain DA [auth FFF] Focus chain GA [auth HHH] Focus chain JA [auth III] Focus chain U [auth AAA] Focus chain Y [auth DDD] Interactions & Density Focus chain DA [auth FFF] Focus chain GA [auth HHH] Focus chain JA [auth III] Focus chain U [auth AAA] Focus chain Y [auth DDD]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain LA [auth JJJ] MOL2 format, chain LA [auth JJJ] mmCIF format, chain LA [auth JJJ]	LA [auth JJJ]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain LA [auth JJJ] Interactions & Density Focus chain LA [auth JJJ]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain MA [auth JJJ] MOL2 format, chain MA [auth JJJ] mmCIF format, chain MA [auth JJJ]	MA [auth JJJ]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain MA [auth JJJ] Interactions & Density Focus chain MA [auth JJJ]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth EEE] SDF format, chain BA [auth EEE] SDF format, chain HA [auth HHH] MOL2 format, chain AA [auth EEE] MOL2 format, chain BA [auth EEE] MOL2 format, chain HA [auth HHH] mmCIF format, chain AA [auth EEE] mmCIF format, chain BA [auth EEE] mmCIF format, chain HA [auth HHH]	AA [auth EEE], BA [auth EEE], HA [auth HHH]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth EEE] Focus chain BA [auth EEE] Focus chain HA [auth HHH] Interactions & Density Focus chain AA [auth EEE] Focus chain BA [auth EEE] Focus chain HA [auth HHH]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain CA [auth EEE] SDF format, chain EA [auth FFF] SDF format, chain FA [auth GGG] SDF format, chain IA [auth HHH] SDF format, chain KA [auth III] SDF format, chain NA [auth JJJ] SDF format, chain V [auth AAA] SDF format, chain W [auth BBB] SDF format, chain X [auth CCC] SDF format, chain Z [auth DDD] MOL2 format, chain CA [auth EEE] MOL2 format, chain EA [auth FFF] MOL2 format, chain FA [auth GGG] MOL2 format, chain IA [auth HHH] MOL2 format, chain KA [auth III] MOL2 format, chain NA [auth JJJ] MOL2 format, chain V [auth AAA] MOL2 format, chain W [auth BBB] MOL2 format, chain X [auth CCC] MOL2 format, chain Z [auth DDD] mmCIF format, chain CA [auth EEE] mmCIF format, chain EA [auth FFF] mmCIF format, chain FA [auth GGG] mmCIF format, chain IA [auth HHH] mmCIF format, chain KA [auth III] mmCIF format, chain NA [auth JJJ] mmCIF format, chain V [auth AAA] mmCIF format, chain W [auth BBB] mmCIF format, chain X [auth CCC] mmCIF format, chain Z [auth DDD]	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		Interactions Focus chain CA [auth EEE] Focus chain EA [auth FFF] Focus chain FA [auth GGG] Focus chain IA [auth HHH] Focus chain KA [auth III] Focus chain NA [auth JJJ] Focus chain V [auth AAA] Focus chain W [auth BBB] Focus chain X [auth CCC] Focus chain Z [auth DDD] Interactions & Density Focus chain CA [auth EEE] Focus chain EA [auth FFF] Focus chain FA [auth GGG] Focus chain IA [auth HHH] Focus chain KA [auth III] Focus chain NA [auth JJJ] Focus chain V [auth AAA] Focus chain W [auth BBB] Focus chain X [auth CCC] Focus chain Z [auth DDD]