9DIW | pdb_00009diw

Crystal structure of the SARS-CoV-2 main protease in complex with covalent tripeptidyl inhibitor NIP-22c

PDB DOI: https://doi.org/10.2210/pdb9DIW/pdb

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

Deposited: 2024-09-06 Released: 2026-03-11
Deposition Author(s): Engel, J.E., Al-Homoudi, A.I., Muczynski, M.D., Brunzelle, J.S., Kovari, L.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: 2.43 Å
R-Value Free:
0.278 (Depositor), 0.277 (DCC)
R-Value Work:
0.202 (Depositor), 0.201 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Similar Free and Complexed Inhibitor Conformations Enhance SARS-CoV-2 3CLpro Inhibitor Efficacy

Muczynski, M.D., Engel, J.E., Al-Homoudi, A.I., Brunzelle, J.S., Kovari, L.C.

To be published.

Macromolecule Content

Total Structure Weight: 34.29 kDa
Atom Count: 2,416
Modeled Residue Count: 309
Deposited Residue Count: 309
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 7	A	305	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b
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
tripeptidyl inhibitor	B	4	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
02J Query on 02J	B	PEPTIDE-LIKE	C₅ H₅ N O₃		--
ALN Query on ALN	B	L-PEPTIDE LINKING	C₁₃ H₁₃ N O₂		ALA

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.43 Å
R-Value Free: 0.278 (Depositor), 0.277 (DCC)
R-Value Work: 0.202 (Depositor), 0.201 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.88	α = 90
b = 53.96	β = 102.22
c = 47.51	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
pointless	data scaling
PHASER	phasing
REFMAC	refinement

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-03-11

Deposition Author(s):

Al-Homoudi, A.I.

Muczynski, M.D.

Brunzelle, J.S.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	4R01AI161570-03

Revision History (Full details and data files)

Version 1.0: 2026-03-11
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.