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

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:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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

View Full Validation Report

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

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.