7IAN | pdb_00007ian

Group deposition of ZIKV NS2B-NS3 protease in complex with inhibitors from ASAP Discovery Consortium -- Crystal Structure of ZIKV NS2B-NS3 protease in complex with ASAP-0029729-001

PDB DOI: https://doi.org/10.2210/pdb7IAN/pdb
Deposition Group: G_1002345 (changed state) | Explore G_1002345

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

Deposited: 2025-04-10 Released: 2025-04-23
Deposition Author(s): Ni, X., Marples, P.G., Godoy, A.S., Koekemoer, L., Aschenbrenner, J.C., Balcomb, B.H., Fairhead, M., Lithgo, R.M., Lee, A., Kenton, N., Thompson, W., Tomlinson, C.W.E., Wild, C., Winokan, M., Williams, E.P., Chandran, A.V., Walsh, M.A., Fearon, D., von Delft, F.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free:
0.265 (Depositor), 0.259 (DCC)
R-Value Work:
0.230 (Depositor), 0.222 (DCC)
R-Value Observed:
0.231 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Group deposition of ZIKV NS2B-NS3 protease in complex with inhibitors from ASAP Discovery Consortium

Ni, X., Marples, P.G., Godoy, A.S., Koekemoer, L., Aschenbrenner, J.C., Balcomb, B.H., Fairhead, M., Lithgo, R.M., Lee, A., Kenton, N., Thompson, W., Tomlinson, C.W.E., Wild, C., Winokan, M., Williams, E.P., Chandran, A.V., Walsh, M.A., Fearon, D., von Delft, F.

To be published.

Macromolecule Content

Total Structure Weight: 23.58 kDa
Atom Count: 1,631
Modeled Residue Count: 195
Deposited Residue Count: 214
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine protease subunit NS2B	A	46	Zika virus	Mutation(s): 0
UniProt
Find proteins for Q32ZE1 (Zika virus) Explore Q32ZE1 Go to UniProtKB: Q32ZE1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q32ZE1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine protease NS3	B	168	Zika virus	Mutation(s): 0 EC: 3.4.21.91 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.4.13 (PDB Primary Data)
UniProt
Find proteins for Q32ZE1 (Zika virus) Explore Q32ZE1 Go to UniProtKB: Q32ZE1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q32ZE1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1B8Y Query on A1B8Y Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	(7R)-N-(2,3-dihydro-1H-isoindol-5-yl)-2,2-difluoro-7-methyl-6-azaspiro[3.4]octane-6-carboxamide C₁₇ H₂₁ F₂ N₃ O AJUFHWAMJUHFGK-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.265 (Depositor), 0.259 (DCC)
R-Value Work: 0.230 (Depositor), 0.222 (DCC)
R-Value Observed: 0.231 (Depositor)

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.595	α = 90
b = 42.595	β = 90
c = 217.31	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-04-23

Deposition Author(s):

Aschenbrenner, J.C.

Tomlinson, C.W.E.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U19AI171399

Revision History (Full details and data files)

Version 1.0: 2025-04-23
Type: Initial release
Version 1.1: 2026-02-18
Changes: Refinement description

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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.