Macromolecule Content

Total Structure Weight: 69.41 kDa
Atom Count: 4921
Residue Count: 596
Unique protein chains: 1

7K0F

1.65 A resolution structure of SARS-CoV-2 3CL protease in complex with a deuterated GC376 alpha-ketoamide analog (compound 5)

DOI: 10.2210/pdb7K0F/pdb

Classification: HYDROLASE
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2020-09-04 Released: 2021-01-13
Deposition Author(s): Lovell, S., Kashipathy, M.M., Battaile, K.P., Chamandi, S.D., Nguyen, H.N., Kim, Y., Chang, K.O., Groutas, W.C.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.225
R-Value Work: 0.180
R-Value Observed: 0.183

wwPDB Validation 3D Report Full Report

Literature

To be determined

Chamandi, S.D., Zhang, J., Kim, Y., Perera, P., Makin, S., Meyerholzm, D., Nguyen, H.N., Kashipathy, M.M., Battaile, K.P., Lovell, S., Perlman, S., Groutas, W.C., Chang, K.O.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A, B	309	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VR4 Query on VR4 Download Ideal Coordinates CCD File SDF format, chain C [A] SDF format, chain D [B] MOL2 format, chain C [A] MOL2 format, chain D [B]	A, B	N-{(2S,3R)-4-(benzylamino)-3-hydroxy-4-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}-N~2~-[(benzyloxy)carbonyl]-L-leucinamide C₂₉ H₃₈ N₄ O₆ MPMTWRHFCLPCDF-OJJQZRKESA-N		Ligand Interaction
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain E [B] MOL2 format, chain E [B]	B	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.225
R-Value Work: 0.180
R-Value Observed: 0.183
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.246	α = 90
b = 98.532	β = 108
c = 58.962	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Deposited Date: 2020-09-04
Released Date: 2021-01-13

Deposition Author(s):

Kashipathy, M.M.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI109039

Revision History

Version 1.0: 2021-01-13
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.