9QSP | pdb_00009qsp

Crystal structure of Zika Virus NS2B-NS3 protease in complex with Z2242050769

PDB DOI: https://doi.org/10.2210/pdb9QSP/pdb

Classification: VIRAL PROTEIN
Organism(s): Zika virus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-04-06 Released: 2026-04-15
Deposition Author(s): Benz, L.S., Becker, F., Janssen, P., Fuesser, F.T., Weiss, M.S., Kuemmel, D., Koch, O.
Funding Organization(s): German Research Foundation (DFG), German Federal Ministry for Education and Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.216 (Depositor), 0.216 (DCC)
R-Value Work:
0.196 (Depositor), 0.196 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Accessing Ultralarge Chemical Spaces via a Sociable Fragment Library: Design and Crystallographic Screening

Janssen, P., Becker, F., Benz, L.S., Fuesser, F.T., Tolmachova, N., Matviiuk, T., Kondratov, I., Weiss, M.S., Kuemmel, D., Koch, O.

To be published.

Macromolecule Content

Total Structure Weight: 24.91 kDa
Atom Count: 1,554
Modeled Residue Count: 189
Deposited Residue Count: 229
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine protease subunit NS2B	A	53	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

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	B	176	Zika virus	Mutation(s): 2
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1JAB (Subject of Investigation/LOI) Query on A1JAB 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]	~{N}-(2,2-dimethylpropyl)pyridin-2-amine C₁₀ H₁₆ N₂ LDKRDTGJDTXAGK-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: 1.40 Å
R-Value Free: 0.216 (Depositor), 0.216 (DCC)
R-Value Work: 0.196 (Depositor), 0.196 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.92	α = 90
b = 42.92	β = 90
c = 215.78	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-04-15

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	KO 4689/5-1
German Research Foundation (DFG)	Germany	FE2166/1-1
German Research Foundation (DFG)	Germany	GRK 2515
German Federal Ministry for Education and Research	Germany	DZIF Flex Fund TTU 02.906