8ZAI | pdb_00008zai

Crystal structure of SADS-CoV main protease in complex with N5084

PDB DOI: https://doi.org/10.2210/pdb8ZAI/pdb

Classification: VIRAL PROTEIN
Organism(s): Swine acute diarrhea syndrome coronavirus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-04-25 Released: 2025-04-30
Deposition Author(s): Zhao, X., Zeng, R., Lei, J.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free:
0.259 (Depositor), 0.252 (DCC)
R-Value Work:
0.215 (Depositor), 0.219 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

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

Literature

Crystal structure of SADS-CoV main protease in complex with N5084

Zhao, X., Zeng, R., Lei, J.

To be published.

Macromolecule Content

Total Structure Weight: 66.11 kDa
Atom Count: 4,585
Modeled Residue Count: 597
Deposited Residue Count: 604
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ORF1ab polyprotein	A, B	302	Swine acute diarrhea syndrome coronavirus	Mutation(s): 0 Gene Names: orf1ab, ORF1ab
UniProt
Find proteins for A0A2P1G738 (Swine acute diarrhea syndrome coronavirus) Explore A0A2P1G738 Go to UniProtKB: A0A2P1G738
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2P1G738
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1L1B (Subject of Investigation/LOI) Query on A1L1B Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	(2~{R})-~{N}-[(1~{S})-1-(4-fluorophenyl)ethyl]-2-[[(2~{R})-2-oxidanylpropanoyl]-(6-phenylpyridin-3-yl)amino]-2-pyridin-3-yl-propanamide C₃₀ H₂₉ F N₄ O₃ GMJWOUHXKFRKLP-KSWJDTNCSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free: 0.259 (Depositor), 0.252 (DCC)
R-Value Work: 0.215 (Depositor), 0.219 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.6	α = 90
b = 72.25	β = 90
c = 177.92	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-04-30

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2021YFF0702004
Ministry of Science and Technology (MoST, China)	China	2022YFC2303701

Revision History (Full details and data files)

Version 1.0: 2025-04-30
Type: Initial release

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.