7B6U | pdb_00007b6u

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

PDB DOI: https://doi.org/10.2210/pdb7B6U/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: 1.90 Å
R-Value Free:
0.173 (Depositor), 0.177 (DCC)
R-Value Work:
0.146 (Depositor), 0.151 (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: 318.95 kDa
Atom Count: 23,317
Modeled Residue Count: 2,654
Deposited Residue Count: 2,760
Unique protein chains: 1

Macromolecules

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| 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 A0ACD6B8T1 (Sheep polyomavirus 1) Explore A0ACD6B8T1 Go to UniProtKB: A0ACD6B8T1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B8T1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K [auth AaA], O [auth DaD], R [auth FaF], U [auth HaH], X [auth JaJ]	3		N/A	Interactions Focus chain K [auth AaA] Focus chain O [auth DaD] Focus chain R [auth FaF] Focus chain U [auth HaH] Focus chain X [auth JaJ] Interactions & Density Focus chain K [auth AaA] Focus chain O [auth DaD] Focus chain R [auth FaF] Focus chain U [auth HaH] Focus chain X [auth JaJ]
Glycosylation Resources
GlyTouCan: G73578JC GlyCosmos: G73578JC GlyGen: G73578JC

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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]	4		N/A	Interactions Focus chain L [auth AdA] Focus chain M [auth BbB] Focus chain N [auth CaC] Focus chain P [auth DdD] Focus chain Q [auth EaE] Focus chain S [auth FdF] Focus chain T [auth GaG] Focus chain V [auth HdH] Focus chain W [auth IaI] Focus chain Y [auth JdJ] Interactions & Density Focus chain L [auth AdA] Focus chain M [auth BbB] Focus chain N [auth CaC] Focus chain P [auth DdD] Focus chain Q [auth EaE] Focus chain S [auth FdF] Focus chain T [auth GaG] Focus chain V [auth HdH] Focus chain W [auth IaI] Focus chain Y [auth JdJ]
Glycosylation Resources
GlyTouCan: G88796WA GlyCosmos: G88796WA GlyGen: G88796WA

Small Molecules

Ligands 4 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 BA [auth BBB] MOL2 format, chain BA [auth BBB] mmCIF format, chain BA [auth BBB]	BA [auth BBB]	N-acetyl-alpha-neuraminic acid C₁₁ H₁₉ N O₉ SQVRNKJHWKZAKO-YRMXFSIDSA-N		Interactions Focus chain BA [auth BBB] Interactions & Density Focus chain BA [auth BBB]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain LA [auth GGG] SDF format, chain OA [auth HHH] MOL2 format, chain LA [auth GGG] MOL2 format, chain OA [auth HHH] mmCIF format, chain LA [auth GGG] mmCIF format, chain OA [auth HHH]	LA [auth GGG], OA [auth HHH]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain LA [auth GGG] Focus chain OA [auth HHH] Interactions & Density Focus chain LA [auth GGG] Focus chain OA [auth HHH]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain AA [auth AAA] SDF format, chain CA [auth BBB] SDF format, chain EA [auth BBB] SDF format, chain FA [auth CCC] SDF format, chain GA [auth DDD] SDF format, chain IA [auth EEE] SDF format, chain JA [auth FFF] SDF format, chain NA [auth GGG] SDF format, chain PA [auth HHH] SDF format, chain QA [auth HHH] SDF format, chain SA [auth III] SDF format, chain UA [auth JJJ] MOL2 format, chain AA [auth AAA] MOL2 format, chain CA [auth BBB] MOL2 format, chain EA [auth BBB] MOL2 format, chain FA [auth CCC] MOL2 format, chain GA [auth DDD] MOL2 format, chain IA [auth EEE] MOL2 format, chain JA [auth FFF] MOL2 format, chain NA [auth GGG] MOL2 format, chain PA [auth HHH] MOL2 format, chain QA [auth HHH] MOL2 format, chain SA [auth III] MOL2 format, chain UA [auth JJJ] mmCIF format, chain AA [auth AAA] mmCIF format, chain CA [auth BBB] mmCIF format, chain EA [auth BBB] mmCIF format, chain FA [auth CCC] mmCIF format, chain GA [auth DDD] mmCIF format, chain IA [auth EEE] mmCIF format, chain JA [auth FFF] mmCIF format, chain NA [auth GGG] mmCIF format, chain PA [auth HHH] mmCIF format, chain QA [auth HHH] mmCIF format, chain SA [auth III] mmCIF format, chain UA [auth JJJ]	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		Interactions Focus chain AA [auth AAA] Focus chain CA [auth BBB] Focus chain EA [auth BBB] Focus chain FA [auth CCC] Focus chain GA [auth DDD] Focus chain IA [auth EEE] Focus chain JA [auth FFF] Focus chain NA [auth GGG] Focus chain PA [auth HHH] Focus chain QA [auth HHH] Focus chain SA [auth III] Focus chain UA [auth JJJ] Interactions & Density Focus chain AA [auth AAA] Focus chain CA [auth BBB] Focus chain EA [auth BBB] Focus chain FA [auth CCC] Focus chain GA [auth DDD] Focus chain IA [auth EEE] Focus chain JA [auth FFF] Focus chain NA [auth GGG] Focus chain PA [auth HHH] Focus chain QA [auth HHH] Focus chain SA [auth III] Focus chain UA [auth JJJ]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain DA [auth BBB] SDF format, chain HA [auth EEE] SDF format, chain KA [auth FFF] SDF format, chain MA [auth GGG] SDF format, chain RA [auth III] SDF format, chain TA [auth III] SDF format, chain Z [auth AAA] MOL2 format, chain DA [auth BBB] MOL2 format, chain HA [auth EEE] MOL2 format, chain KA [auth FFF] MOL2 format, chain MA [auth GGG] MOL2 format, chain RA [auth III] MOL2 format, chain TA [auth III] MOL2 format, chain Z [auth AAA] mmCIF format, chain DA [auth BBB] mmCIF format, chain HA [auth EEE] mmCIF format, chain KA [auth FFF] mmCIF format, chain MA [auth GGG] mmCIF format, chain RA [auth III] mmCIF format, chain TA [auth III] mmCIF format, chain Z [auth AAA]	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		Interactions Focus chain DA [auth BBB] Focus chain HA [auth EEE] Focus chain KA [auth FFF] Focus chain MA [auth GGG] Focus chain RA [auth III] Focus chain TA [auth III] Focus chain Z [auth AAA] Interactions & Density Focus chain DA [auth BBB] Focus chain HA [auth EEE] Focus chain KA [auth FFF] Focus chain MA [auth GGG] Focus chain RA [auth III] Focus chain TA [auth III] Focus chain Z [auth AAA]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900046 Query on PRD_900046	K [auth AaA], O [auth DaD], R [auth FaF], U [auth HaH], X [auth JaJ]	6'-sialyl-N-acetyllactosamine	Oligosaccharide / Glycan component		Interactions Focus chain K [auth AaA] Focus chain O [auth DaD] Focus chain R [auth FaF] Focus chain U [auth HaH] Focus chain X [auth JaJ] Interactions & Density Focus chain K [auth AaA] Focus chain O [auth DaD] Focus chain R [auth FaF] Focus chain U [auth HaH] Focus chain X [auth JaJ]