8RS7 | pdb_00008rs7

Crystal structure of Zika Virus NS2B-NS3 protease in complex with an allosteric inhibitor

PDB DOI: https://doi.org/10.2210/pdb8RS7/pdb

Classification: HYDROLASE
Organism(s): Zika virus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-01-24 Released: 2025-11-05
Deposition Author(s): Ontoria, J.M., Torrente, E.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.18 Å
R-Value Free:
0.330 (Depositor), 0.331 (DCC)
R-Value Work:
0.281 (Depositor), 0.281 (DCC)
R-Value Observed:
0.283 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Zika Virus NS2B-NS3 protease in complex with an allosteric inhibitor

Ontoria, J.M., Torrente, E.

To be published.

Macromolecule Content

Total Structure Weight: 49.55 kDa
Atom Count: 2,520
Modeled Residue Count: 319
Deposited Residue Count: 460
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	A, B	230	Zika virus	Mutation(s): 0
UniProt
Find proteins for A0A140DLX4 (Zika virus) Explore A0A140DLX4 Go to UniProtKB: A0A140DLX4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A140DLX4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1H3F (Subject of Investigation/LOI) Query on A1H3F Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	1-[3-[[5-[4-[2-(dimethylamino)ethoxy]-6-methyl-pyrimidin-5-yl]pyridin-2-yl]methyl]-1,2,3-oxadiazol-3-ium-5-yl]-3-[3-(trifluoromethyl)phenyl]urea C₂₅ H₂₆ F₃ N₈ O₃ RCCQGUWPTDCULB-UHFFFAOYSA-O		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: 3.18 Å
R-Value Free: 0.330 (Depositor), 0.331 (DCC)
R-Value Work: 0.281 (Depositor), 0.281 (DCC)
R-Value Observed: 0.283 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.688	α = 90
b = 90.351	β = 90
c = 96.189	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
pointless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-11-05

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-11-05
Type: Initial release
Version 1.1: 2025-12-03
Changes: Structure summary

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.