7B6T | pdb_00007b6t

Sheep Polyomavirus VP1 in complex with 10 mM globo-N-tetraose

PDB DOI: https://doi.org/10.2210/pdb7B6T/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: 1.70 Å
R-Value Free:
0.165 (Depositor), 0.170 (DCC)
R-Value Work:
0.143 (Depositor), 0.150 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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: 312.31 kDa
Atom Count: 24,010
Modeled Residue Count: 2,645
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-beta-D-galactopyranose-(1-3)-alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose	K [auth AaA], M [auth CaC], O [auth FaF], P [auth HaH]	3		N/A	Interactions Focus chain K [auth AaA] Focus chain M [auth CaC] Focus chain O [auth FaF] Focus chain P [auth HaH] Interactions & Density Focus chain K [auth AaA] Focus chain M [auth CaC] Focus chain O [auth FaF] Focus chain P [auth HaH]
Glycosylation Resources
GlyTouCan: G30239EK GlyCosmos: G30239EK GlyGen: G30239EK

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-alpha-D-galactopyranose	L [auth BaB], N [auth DaD], Q [auth JaJ]	2		N/A	Interactions Focus chain L [auth BaB] Focus chain N [auth DaD] Focus chain Q [auth JaJ] Interactions & Density Focus chain L [auth BaB] Focus chain N [auth DaD] Focus chain Q [auth JaJ]
Glycosylation Resources
GlyTouCan: G71661JQ GlyCosmos: G71661JQ GlyGen: G71661JQ

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain X [auth BBB] SDF format, chain W [auth BBB] SDF format, chain V [auth BBB] MOL2 format, chain X [auth BBB] MOL2 format, chain W [auth BBB] MOL2 format, chain V [auth BBB] mmCIF format, chain X [auth BBB] mmCIF format, chain W [auth BBB] mmCIF format, chain V [auth BBB]	V [auth BBB], W [auth BBB], X [auth BBB]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain V [auth BBB] Focus chain W [auth BBB] Focus chain X [auth BBB] Interactions & Density Focus chain V [auth BBB] Focus chain W [auth BBB] Focus chain X [auth BBB]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain WA [auth GGG] SDF format, chain NA [auth EEE] SDF format, chain GB [auth III] MOL2 format, chain WA [auth GGG] MOL2 format, chain NA [auth EEE] MOL2 format, chain GB [auth III] mmCIF format, chain WA [auth GGG] mmCIF format, chain NA [auth EEE] mmCIF format, chain GB [auth III]	GB [auth III], NA [auth EEE], WA [auth GGG]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain GB [auth III] Focus chain NA [auth EEE] Focus chain WA [auth GGG] Interactions & Density Focus chain GB [auth III] Focus chain NA [auth EEE] Focus chain WA [auth GGG]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain SA [auth FFF] SDF format, chain R [auth AAA] SDF format, chain LA [auth EEE] SDF format, chain IA [auth DDD] SDF format, chain EA [auth CCC] SDF format, chain BA [auth CCC] MOL2 format, chain SA [auth FFF] MOL2 format, chain R [auth AAA] MOL2 format, chain LA [auth EEE] MOL2 format, chain IA [auth DDD] MOL2 format, chain EA [auth CCC] MOL2 format, chain BA [auth CCC] mmCIF format, chain SA [auth FFF] mmCIF format, chain R [auth AAA] mmCIF format, chain LA [auth EEE] mmCIF format, chain IA [auth DDD] mmCIF format, chain EA [auth CCC] mmCIF format, chain BA [auth CCC]	BA [auth CCC] EA [auth CCC] IA [auth DDD] LA [auth EEE] R [auth AAA] BA [auth CCC], EA [auth CCC], IA [auth DDD], LA [auth EEE], R [auth AAA], SA [auth FFF]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain BA [auth CCC] Focus chain EA [auth CCC] Focus chain IA [auth DDD] Focus chain LA [auth EEE] Focus chain R [auth AAA] Focus chain SA [auth FFF] Interactions & Density Focus chain BA [auth CCC] Focus chain EA [auth CCC] Focus chain IA [auth DDD] Focus chain LA [auth EEE] Focus chain R [auth AAA] Focus chain SA [auth FFF]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain ZA [auth HHH] SDF format, chain Y [auth BBB] SDF format, chain U [auth BBB] SDF format, chain TA [auth FFF] SDF format, chain RA [auth FFF] SDF format, chain QA [auth FFF] SDF format, chain NB [auth JJJ] SDF format, chain MB [auth JJJ] SDF format, chain MA [auth EEE] SDF format, chain IB [auth III] SDF format, chain HB [auth III] SDF format, chain FB [auth III] SDF format, chain FA [auth CCC] SDF format, chain DA [auth CCC] SDF format, chain CB [auth HHH] SDF format, chain CA [auth CCC] SDF format, chain BB [auth HHH] SDF format, chain AB [auth HHH] MOL2 format, chain ZA [auth HHH] MOL2 format, chain Y [auth BBB] MOL2 format, chain U [auth BBB] MOL2 format, chain TA [auth FFF] MOL2 format, chain RA [auth FFF] MOL2 format, chain QA [auth FFF] MOL2 format, chain NB [auth JJJ] MOL2 format, chain MB [auth JJJ] MOL2 format, chain MA [auth EEE] MOL2 format, chain IB [auth III] MOL2 format, chain HB [auth III] MOL2 format, chain FB [auth III] MOL2 format, chain FA [auth CCC] MOL2 format, chain DA [auth CCC] MOL2 format, chain CB [auth HHH] MOL2 format, chain CA [auth CCC] MOL2 format, chain BB [auth HHH] MOL2 format, chain AB [auth HHH] mmCIF format, chain ZA [auth HHH] mmCIF format, chain Y [auth BBB] mmCIF format, chain U [auth BBB] mmCIF format, chain TA [auth FFF] mmCIF format, chain RA [auth FFF] mmCIF format, chain QA [auth FFF] mmCIF format, chain NB [auth JJJ] mmCIF format, chain MB [auth JJJ] mmCIF format, chain MA [auth EEE] mmCIF format, chain IB [auth III] mmCIF format, chain HB [auth III] mmCIF format, chain FB [auth III] mmCIF format, chain FA [auth CCC] mmCIF format, chain DA [auth CCC] mmCIF format, chain CB [auth HHH] mmCIF format, chain CA [auth CCC] mmCIF format, chain BB [auth HHH] mmCIF format, chain AB [auth HHH]	AB [auth HHH] BB [auth HHH] CA [auth CCC] CB [auth HHH] DA [auth CCC] AB [auth HHH], BB [auth HHH], CA [auth CCC], CB [auth HHH], DA [auth CCC], FA [auth CCC], FB [auth III], HB [auth III], IB [auth III], MA [auth EEE], MB [auth JJJ], NB [auth JJJ], QA [auth FFF], RA [auth FFF], TA [auth FFF], U [auth BBB], Y [auth BBB], ZA [auth HHH]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AB [auth HHH] Focus chain BB [auth HHH] Focus chain CA [auth CCC] Focus chain CB [auth HHH] Focus chain DA [auth CCC] Focus chain FA [auth CCC] Focus chain FB [auth III] Focus chain HB [auth III] Focus chain IB [auth III] Focus chain MA [auth EEE] Focus chain MB [auth JJJ] Focus chain NB [auth JJJ] Focus chain QA [auth FFF] Focus chain RA [auth FFF] Focus chain TA [auth FFF] Focus chain U [auth BBB] Focus chain Y [auth BBB] Focus chain ZA [auth HHH] Interactions & Density Focus chain AB [auth HHH] Focus chain BB [auth HHH] Focus chain CA [auth CCC] Focus chain CB [auth HHH] Focus chain DA [auth CCC] Focus chain FA [auth CCC] Focus chain FB [auth III] Focus chain HB [auth III] Focus chain IB [auth III] Focus chain MA [auth EEE] Focus chain MB [auth JJJ] Focus chain NB [auth JJJ] Focus chain QA [auth FFF] Focus chain RA [auth FFF] Focus chain TA [auth FFF] Focus chain U [auth BBB] Focus chain Y [auth BBB] Focus chain ZA [auth HHH]
K Query on K Download Ideal Coordinates CCD File SDF format, chain VA [auth FFF] SDF format, chain T [auth AAA] SDF format, chain PB [auth JJJ] SDF format, chain PA [auth EEE] SDF format, chain LB [auth III] SDF format, chain KA [auth DDD] SDF format, chain HA [auth CCC] SDF format, chain EB [auth HHH] SDF format, chain AA [auth BBB] MOL2 format, chain VA [auth FFF] MOL2 format, chain T [auth AAA] MOL2 format, chain PB [auth JJJ] MOL2 format, chain PA [auth EEE] MOL2 format, chain LB [auth III] MOL2 format, chain KA [auth DDD] MOL2 format, chain HA [auth CCC] MOL2 format, chain EB [auth HHH] MOL2 format, chain AA [auth BBB] mmCIF format, chain VA [auth FFF] mmCIF format, chain T [auth AAA] mmCIF format, chain PB [auth JJJ] mmCIF format, chain PA [auth EEE] mmCIF format, chain LB [auth III] mmCIF format, chain KA [auth DDD] mmCIF format, chain HA [auth CCC] mmCIF format, chain EB [auth HHH] mmCIF format, chain AA [auth BBB]	AA [auth BBB] EB [auth HHH] HA [auth CCC] KA [auth DDD] LB [auth III] AA [auth BBB], EB [auth HHH], HA [auth CCC], KA [auth DDD], LB [auth III], PA [auth EEE], PB [auth JJJ], T [auth AAA], VA [auth FFF]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain AA [auth BBB] Focus chain EB [auth HHH] Focus chain HA [auth CCC] Focus chain KA [auth DDD] Focus chain LB [auth III] Focus chain PA [auth EEE] Focus chain PB [auth JJJ] Focus chain T [auth AAA] Focus chain VA [auth FFF] Interactions & Density Focus chain AA [auth BBB] Focus chain EB [auth HHH] Focus chain HA [auth CCC] Focus chain KA [auth DDD] Focus chain LB [auth III] Focus chain PA [auth EEE] Focus chain PB [auth JJJ] Focus chain T [auth AAA] Focus chain VA [auth FFF]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain Z [auth BBB] SDF format, chain YA [auth GGG] SDF format, chain XA [auth GGG] SDF format, chain UA [auth FFF] SDF format, chain S [auth AAA] SDF format, chain OB [auth JJJ] SDF format, chain OA [auth EEE] SDF format, chain KB [auth III] SDF format, chain JB [auth III] SDF format, chain JA [auth DDD] SDF format, chain GA [auth CCC] SDF format, chain DB [auth HHH] MOL2 format, chain Z [auth BBB] MOL2 format, chain YA [auth GGG] MOL2 format, chain XA [auth GGG] MOL2 format, chain UA [auth FFF] MOL2 format, chain S [auth AAA] MOL2 format, chain OB [auth JJJ] MOL2 format, chain OA [auth EEE] MOL2 format, chain KB [auth III] MOL2 format, chain JB [auth III] MOL2 format, chain JA [auth DDD] MOL2 format, chain GA [auth CCC] MOL2 format, chain DB [auth HHH] mmCIF format, chain Z [auth BBB] mmCIF format, chain YA [auth GGG] mmCIF format, chain XA [auth GGG] mmCIF format, chain UA [auth FFF] mmCIF format, chain S [auth AAA] mmCIF format, chain OB [auth JJJ] mmCIF format, chain OA [auth EEE] mmCIF format, chain KB [auth III] mmCIF format, chain JB [auth III] mmCIF format, chain JA [auth DDD] mmCIF format, chain GA [auth CCC] mmCIF format, chain DB [auth HHH]	DB [auth HHH] GA [auth CCC] JA [auth DDD] JB [auth III] KB [auth III] DB [auth HHH], GA [auth CCC], JA [auth DDD], JB [auth III], KB [auth III], OA [auth EEE], OB [auth JJJ], S [auth AAA], UA [auth FFF], XA [auth GGG], YA [auth GGG], Z [auth BBB]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain DB [auth HHH] Focus chain GA [auth CCC] Focus chain JA [auth DDD] Focus chain JB [auth III] Focus chain KB [auth III] Focus chain OA [auth EEE] Focus chain OB [auth JJJ] Focus chain S [auth AAA] Focus chain UA [auth FFF] Focus chain XA [auth GGG] Focus chain YA [auth GGG] Focus chain Z [auth BBB] Interactions & Density Focus chain DB [auth HHH] Focus chain GA [auth CCC] Focus chain JA [auth DDD] Focus chain JB [auth III] Focus chain KB [auth III] Focus chain OA [auth EEE] Focus chain OB [auth JJJ] Focus chain S [auth AAA] Focus chain UA [auth FFF] Focus chain XA [auth GGG] Focus chain YA [auth GGG] Focus chain Z [auth BBB]