8GVD

SARS-CoV-2 Mpro in complex with D-4-38

• PDB DOI: https://doi.org/10.2210/pdb8GVD/pdb

• Classification: HYDROLASE
• Organism(s): Severe acute respiratory syndrome coronavirus 2, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-09-14 Released: 2023-09-20 
• Deposition Author(s): Liu, M., Huang, H.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.248 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 

Literature

SARS-CoV-2 Mpro in complex with D-4-38

Liu, M., Huang, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 34.23 kDa 
• Atom Count: 2,541 
• Modelled Residue Count: 310 
• Deposited Residue Count: 310 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE	B	4	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
0A9	B	L-PEPTIDE LINKING	C10 H13 N O2		PHE

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.248 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 
• Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.052	α = 90
b = 53.324	β = 100.84
c = 112.859	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
CrysalisPro	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-09-20 
Deposition Author(s): Liu, M., Huang, H.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-09-20
  Type: Initial release
  
• Version 1.1: 2023-11-15
  Changes: Data collection