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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free:
0.244 (Depositor), 0.253 (DCC)
R-Value Work:
0.199 (Depositor), 0.206 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8T7Y

This is version 1.0 of the entry. See complete history.

Literature

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

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

To be published.

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

Find similar proteins by:

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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 Query on 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 Query on PRD_002331	C, D [auth E]	Chymostatin A (bound form)	Oligopeptide / Enzyme inhibitor		Interactions Focus chain C Focus chain D [auth E] Interactions & Density Focus chain C Focus chain D [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.244 (Depositor), 0.253 (DCC)
R-Value Work: 0.199 (Depositor), 0.206 (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

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-06-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.