9YP1 | pdb_00009yp1

Rabbit Hemorrhagic Disease Virus Czech P domain

PDB DOI: https://doi.org/10.2210/pdb9YP1/pdb

Classification: VIRAL PROTEIN
Organism(s): Rabbit hemorrhagic disease virus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-10-13 Released: 2025-12-03
Deposition Author(s): Kara, D., Pancera, M., Hansman, G.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.37 Å
R-Value Free:
0.172 (Depositor), 0.172 (DCC)
R-Value Work:
0.150 (Depositor), 0.150 (DCC)
R-Value Observed:
0.151 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural insights into a broadly reactive nanobody that binds pathogenic and non-pathogenic lagoviruses.

Kara, D., Pancera, M., Hassanzadeh-Ghassabeh, G., Schoonooghe, S., Masic, V., Hartley-Tassell, L., Mishra, B.P., Ve, T., Haselhorst, T., von Itzstein, M., Hansman, G.S.

(2026) J Virol 100: e0199025-e0199025

PubMed: 41504443 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1128/jvi.01990-25
Primary Citation Related Structures:
9YP1, 9YP2

Organizational Affiliation

Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA.

Macromolecule Content

Total Structure Weight: 71.31 kDa
Atom Count: 5,808
Modeled Residue Count: 669
Deposited Residue Count: 678
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A [auth B], B [auth A]	339	Rabbit hemorrhagic disease virus	Mutation(s): 0 Gene Names: VP60
UniProt
Find proteins for V5K505 (Rabbit hemorrhagic disease virus) Explore V5K505 Go to UniProtKB: V5K505
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	V5K505
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NHE Query on NHE Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C₈ H₁₇ N O₃ S MKWKNSIESPFAQN-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A] mmCIF format, chain O [auth A]	O [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A] mmCIF format, chain P [auth A]	P [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Interactions & Density Focus chain P [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth B] SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth A] SDF format, chain N [auth A] MOL2 format, chain C [auth B] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] mmCIF format, chain C [auth B] mmCIF format, chain D [auth B] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A]	C [auth B] D [auth B] E [auth B] F [auth B] G [auth B] C [auth B], D [auth B], E [auth B], F [auth B], G [auth B], H [auth B], J [auth B], K [auth B], L [auth B], M [auth A], N [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth A] Focus chain N [auth A]