Macromolecule Content

Total Structure Weight: 68.76 kDa
Atom Count: 5306
Residue Count: 601
Unique protein chains: 1

7C7P

Crystal structure of the SARS-CoV-2 main protease in complex with Telaprevir

DOI: 10.2210/pdb7C7P/pdb

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-05-26 Released: 2020-07-29
Deposition Author(s): Zeng, R., Qiao, J.X., Wang, Y.F., Li, Y.S., Yao, R., Yang, S.Y., Lei, J.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free: 0.216
R-Value Work: 0.174
R-Value Observed: 0.176

wwPDB Validation 3D Report Full Report

Literature

Crystal structure of the SARS-CoV-2 main protease in complex with Telaprevir

Qiao, J.X., Zeng, R., Wang, Y.F., Li, Y.S., Yao, R., Zhou, Y.L., Chen, P., Lei, J., Yang, S.Y.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
main protease	A, B	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b EC: 3.4.22.69 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt), 2.1.1 (UniProt)
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SV6 Query on SV6 Download Ideal Coordinates CCD File SDF format, chain C [A] MOL2 format, chain C [A]	A	(1S,3aR,6aS)-2-[(2S)-2-({(2S)-2-cyclohexyl-2-[(pyrazin-2-ylcarbonyl)amino]acetyl}amino)-3,3-dimethylbutanoyl]-N-[(2R,3S)-1-(cyclopropylamino)-2-hydroxy-1-oxohexan-3-yl]octahydrocyclopenta[c]pyrrole-1-carboxamide C₃₆ H₅₅ N₇ O₆ FTZGWEAUHOMNIG-FJRGXGLZSA-N		Ligand Interaction
FK3 Query on FK3 Download Ideal Coordinates CCD File SDF format, chain E [B] MOL2 format, chain E [B]	B	(3~{S},3~{a}~{S},6~{a}~{R})-~{N}-[(2~{R},3~{S})-1-(cyclopropylamino)-2-oxidanyl-1-oxidanylidene-hexan-3-yl]-2-methanoyl-3,3~{a},4,5,6,6~{a}-hexahydro-1~{H}-cyclopenta[c]pyrrole-3-carboxamide C₁₈ H₂₉ N₃ O₄ QNPKORKCVLMDCG-VLVIQNCWSA-N		Ligand Interaction
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [A] SDF format, chain F [B] MOL2 format, chain D [A] MOL2 format, chain F [B]	A, B	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002448 (SV6) Query on PRD_002448	A	TELAPREVIR, bound form	Peptide-like / Antiviral		--

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free: 0.216
R-Value Work: 0.174
R-Value Observed: 0.176
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.907	α = 90
b = 98.731	β = 90
c = 103.487	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Deposited Date: 2020-05-26
Released Date: 2020-07-29

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	2020YFS0010/HX2019nCoV039

Revision History

Version 1.0: 2020-07-29
Type: Initial release

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.