7MAT | pdb_00007mat

SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor dFFR

• PDB DOI: https://doi.org/10.2210/pdb7MAT/pdb

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


• Deposited: 2021-03-31 Released: 2022-10-12 
• Deposition Author(s): Lockbaum, G.J., Schiffer, C.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.74 Å
• R-Value Free: 
  0.260 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor dFFR

Lockbaum, G.J., Schiffer, C.A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 68.75 kDa 
• Atom Count: 4,600 
• Modeled Residue Count: 609 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A, B	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
H37 (Subject of Investigation/LOI)	C [auth A], E [auth B]	D-phenylalanyl-N-[(3S)-6-carbamimidamido-1-chloro-2-oxohexan-3-yl]-L-phenylalaninamide C25 H33 Cl N6 O3 PJFSUJMJVYGASC-HKBOAZHASA-N
SO4	D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001160 (H37)	C [auth A], E [auth B]	D-PHENYLALANYL-N-[(3S)-6-CARBAMIMIDAMIDO-1-CHLORO-2-OXOHEXAN-3-YL]-L-PHENYLALANINAMIDE	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.74 Å
• R-Value Free:  0.260 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.973	α = 90
b = 105.769	β = 104
c = 54.389	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHASER	phasing
PHENIX	refinement
Coot	model building
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-10-12 
Deposition Author(s): Lockbaum, G.J., Schiffer, C.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P01-GM109767

Revision History  

• Version 1.0: 2022-10-12
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary