8X5P | pdb_00008x5p

Crystal structure of MjHKUr-CoV spike HR1 in complex with EK1 peptide

PDB DOI: https://doi.org/10.2210/pdb8X5P/pdb

Classification: VIRAL PROTEIN
Organism(s): Coronavirus HKU23
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-11-17 Released: 2025-05-21
Deposition Author(s): Zhu, Y., Yang, X., Sun, F.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free:
0.284 (Depositor), 0.282 (DCC)
R-Value Work:
0.229 (Depositor), 0.231 (DCC)
R-Value Observed:
0.232 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 8X5P

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

Literature

Fusion mechanism of MjHKUr-CoV spike and its entry inhibitor

Zhu, Y., Sun, F., Lu, L.

To be published.

Macromolecule Content

Total Structure Weight: 71.73 kDa
Atom Count: 4,440
Modeled Residue Count: 553
Deposited Residue Count: 666
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S2,EK1 peptide	A, B, C, D, E A, B, C, D, E, F	111	Coronavirus HKU23	Mutation(s): 0 Gene Names: S
UniProt
Find proteins for Q0Q4F2 (Bat coronavirus 133/2005) Explore Q0Q4F2 Go to UniProtKB: Q0Q4F2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q0Q4F2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth F] SDF format, chain G [auth A] MOL2 format, chain H [auth F] MOL2 format, chain G [auth A] mmCIF format, chain H [auth F] mmCIF format, chain G [auth A]	G [auth A], H [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free: 0.284 (Depositor), 0.282 (DCC)
R-Value Work: 0.229 (Depositor), 0.231 (DCC)
R-Value Observed: 0.232 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.373	α = 90
b = 42.344	β = 98.22
c = 169.294	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-05-21

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-05-21
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.