9BOO

Crystal structure of MERS-CoV Nsp5 in complex with PF-07817883

PDB DOI: https://doi.org/10.2210/pdb9BOO/pdb

Classification: VIRAL PROTEIN
Organism(s): Middle East respiratory syndrome-related coronavirus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-05-05 Released: 2024-08-07
Deposition Author(s): Chen, P., Arutyunova, E., Lemieux, M.J.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.195
R-Value Work: 0.175
R-Value Observed: 0.176

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A Structural Comparison of Oral SARS-CoV-2 Drug Candidate Ibuzatrelvir Complexed with the Main Protease (Mpro) of SARS-CoV-2 and MERS-CoV

Chen, P., Van Oers, T.J., Arutyunova, E., Fischer, C., Wang, C., Lamer, T., van Belkum, M.J., Young, H.S., Vederas, J.C., Lemieux, M.J.

(2024) JACS Au

DOI: https://doi.org/10.1021/jacsau.4c00508

Macromolecule Content

Total Structure Weight: 33.85 kDa
Atom Count: 2,651
Modelled Residue Count: 304
Deposited Residue Count: 306
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A	306	Middle East respiratory syndrome-related coronavirus	Mutation(s): 0 Gene Names: 1a EC: 3.4.22.69
UniProt
Find proteins for K9N638 (Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012)) Explore K9N638 Go to UniProtKB: K9N638
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	K9N638
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YDL (Subject of Investigation/LOI) Query on YDL Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	N-(methoxycarbonyl)-3-methyl-L-valyl-(4R)-N-{(1Z,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-4-(trifluoromethyl)-L-prolinamide C₂₁ H₃₂ F₃ N₅ O₅ DTVPKRIYQXLPLE-AIEDFZFUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.195
R-Value Work: 0.175
R-Value Observed: 0.176
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.153	α = 90
b = 57.4	β = 113
c = 49.004	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-08-07

Deposition Author(s):

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History (Full details and data files)

Version 1.0: 2024-08-07
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 R01GM133198.