9NSM | pdb_00009nsm

Crystal structure of the bat rotavirus apo P[10] VP8* receptor binding domain at 1.85 angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb9NSM/pdb

Classification: VIRAL PROTEIN
Organism(s): Rotavirus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-03-17 Released: 2025-03-26
Deposition Author(s): Kennedy, M.A., Ni, S., Li, F., Wang, D., Soni, S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.213 (Depositor), 0.211 (DCC)
R-Value Work:
0.195 (Depositor), 0.195 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of the bat rotavirus apo P[10] VP8* receptor binding domain at 1.85 angstrom resolution

Kennedy, M.A., Ni, S., Li, F., Wang, D., Soni, S.

To be published.

Macromolecule Content

Total Structure Weight: 60.06 kDa
Atom Count: 4,207
Modeled Residue Count: 504
Deposited Residue Count: 531
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer capsid protein VP8*	A, B, C	177	Rotavirus	Mutation(s): 0 Gene Names: VP4
UniProt
Find proteins for A0A7R7E052 (Rotavirus A) Explore A0A7R7E052 Go to UniProtKB: A0A7R7E052
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7R7E052
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain P [auth B] SDF format, chain S [auth C] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain P [auth B] MOL2 format, chain S [auth C] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain P [auth B] mmCIF format, chain S [auth C]	I [auth A], J [auth A], P [auth B], S [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth B] Focus chain S [auth C] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth B] Focus chain S [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain K [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], Q [auth C], R [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C]