9Y51 | pdb_00009y51

PanDDA analysis -- Crystal Structure of Zika virus NS3 Helicase in complex with Z1563512128

PDB DOI: https://doi.org/10.2210/pdb9Y51/pdb

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

Deposited: 2025-09-04 Released: 2025-09-17
Deposition Author(s): Godoy, A.S., Mesquita, N., Oliva, G.
Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free:
0.213 (Depositor), 0.213 (DCC)
R-Value Work:
0.174 (Depositor), 0.175 (DCC)
R-Value Observed:
0.176 (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

PanDDA analysis -- Crystal Structure of Zika virus NS3 Helicase in complex with Z1563512128

Godoy, A.S., Mesquita, N., Oliva, G.

To be published.

Macromolecule Content

Total Structure Weight: 49.71 kDa
Atom Count: 3,850
Modeled Residue Count: 435
Deposited Residue Count: 435
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zika virus NS3 helicase domain	A	435	Zika virus	Mutation(s): 0 EC: 3.6.4.13
UniProt
Find proteins for Q32ZE1 (Zika virus) Explore Q32ZE1 Go to UniProtKB: Q32ZE1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q32ZE1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
M0J (Subject of Investigation/LOI) Query on M0J Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	N-[(2S)-2-hydroxypropyl]-N'-phenylurea C₁₀ H₁₄ N₂ O₂ XEAXHIGGZMUNSO-QMMMGPOBSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]