8T7Y | pdb_00008t7y

Structure of SARS CoV-2 main protease in complex with Chymostatin.

• PDB DOI: https://doi.org/10.2210/pdb8T7Y/pdb

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


• Deposited: 2023-06-21 Released: 2024-06-26 
• Deposition Author(s): Terzyan, S., Yarla, N., Rao, C.V., Mooers, B.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.244 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Structure of SARS CoV-2 main protease in complex with Chymostatin.

Terzyan, S., Yarla, N., Rao, C.V., Mooers, B.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Macromolecule Content 

• Total Structure Weight: 68.87 kDa 
• Atom Count: 5,059 
• Modeled Residue Count: 618 
• Deposited Residue Count: 620 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Chymostatin A (bound form)	C, D [auth E]	4	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PHL	C, D [auth E]	L-PEPTIDE LINKING	C9 H13 N O		PHE

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002331	C, D [auth E]	Chymostatin A (bound form)	Oligopeptide / Enzyme inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.244 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.184	α = 90
b = 105.231	β = 101.59
c = 54.473	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data scaling
HKL-3000	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-26 
Deposition Author(s): Terzyan, S., Yarla, N., Rao, C.V., Mooers, B.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-06-26
  Type: Initial release