Macromolecule Content

Total Structure Weight: 67.00 kDa
Atom Count: 5566
Modelled Residue Count: 608
Deposited Residue Count: 612
Unique protein chains: 1

2YNA

Crystal structure of the main protease of coronavirus HKU4

PDB DOI: 10.2210/pdb2YNA/pdb

Classification: HYDROLASE
Organism(s): Tylonycteris bat coronavirus HKU4
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-10-13 Released: 2013-10-23
Deposition Author(s): Ma, Q., Xiao, Y., Hilgenfeld, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.175
R-Value Work: 0.157
R-Value Observed: 0.158

wwPDB Validation 3D Report Full Report

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

Literature

Inhibitor for the Main Protease of Coronavirus Hku4

Ma, Q., Xiao, Y., Hilgenfeld, R.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-LIKE PROTEINASE	A, B	306	Tylonycteris bat coronavirus HKU4	Mutation(s): 0 Gene Names: 1a EC: 3.4.22.69 (PDB Primary Data), 3.4.22 (PDB Primary Data), 3.4.19.12 (UniProt)
UniProt
Find proteins for P0C6T4 (Bat coronavirus HKU4) Explore P0C6T4 Go to UniProtKB: P0C6T4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C6T4
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 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 B] SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B]	E [auth A], G [auth B], H [auth B], I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Ligand Interaction
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B]	C [auth A], F [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.175
R-Value Work: 0.157
R-Value Observed: 0.158
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.624	α = 90
b = 79.624	β = 90
c = 178.37	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
AutoPROC	data reduction
XDS	data reduction
AutoPROC	data scaling
XDS	data scaling
SCALA	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2012-10-13
Released Date: 2013-10-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-10-23
Type: Initial release
Version 1.1: 2019-05-15
Changes: Data collection, Experimental preparation, Other

RCSB PDB is funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.