7WQJ | pdb_00007wqj

Crystal structure of MERS main protease in complex with PF07304814

PDB DOI: https://doi.org/10.2210/pdb7WQJ/pdb

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

Deposited: 2022-01-25 Released: 2022-08-24
Deposition Author(s): Lin, C., Zhang, J., Li, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.290 (Depositor), 0.290 (DCC)
R-Value Work:
0.224 (Depositor), 0.220 (DCC)
R-Value Observed:
0.231 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural Basis of Main Proteases of Coronavirus Bound to Drug Candidate PF-07304814

Li, J., Lin, C., Zhou, X., Zhong, F., Zeng, P., McCormick, P.J., Jiang, H., Zhang, J.

(2022) J Mol Biology 434: 167706

DOI: https://doi.org/10.1016/j.jmb.2022.167706

Macromolecule Content

Total Structure Weight: 66.06 kDa
Atom Count: 4,565
Modeled Residue Count: 599
Deposited Residue Count: 600
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	A, B	300	Middle East respiratory syndrome-related coronavirus	Mutation(s): 0 EC: 3.4.19.12 (PDB Primary Data), 3.4.22.69 (PDB Primary Data)
UniProt
Find proteins for K9N7C7 (Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012)) Explore K9N7C7 Go to UniProtKB: K9N7C7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	K9N7C7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
80I (Subject of Investigation/LOI) Query on 80I Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	[(3~{S})-3-[[(2~{S})-2-[(4-methoxy-1~{H}-indol-2-yl)carbonylamino]-4-methyl-pentanoyl]amino]-2-oxidanylidene-4-[(3~{R})-2-oxidanylidene-3,4-dihydropyrrol-3-yl]butyl] dihydrogen phosphate C₂₄ H₃₃ N₄ O₉ P FQKALOFOWPDTED-WBAXXEDZSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.290 (Depositor), 0.290 (DCC)
R-Value Work: 0.224 (Depositor), 0.220 (DCC)
R-Value Observed: 0.231 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.515	α = 90
b = 92.771	β = 90
c = 97.703	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-08-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-08-24
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

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.