8V7R | pdb_00008v7r

PanDDA analysis -- Crystal Structure of Zika virus NS3 Helicase in complex with Z56772132

PDB DOI: https://doi.org/10.2210/pdb8V7R/pdb

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

Deposited: 2023-12-04 Released: 2023-12-20
Deposition Author(s): Godoy, A.S., Noske, G.D., Fairhead, M., Lithgo, R.M., Koekemoer, L., Aschenbrenner, J.C., Balcomb, B.H., Marples, P.G., Ni, X., Tomlinson, C.W.E., Wild, C., Mesquita, N.C.M.R., Oliva, G., Fearon, D., Walsh, M.A., von Delft, F.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Sao Paulo Research Foundation (FAPESP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.41 Å
R-Value Free:
0.206 (Depositor), 0.221 (DCC)
R-Value Work:
0.168 (Depositor)
R-Value Observed:
0.170 (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 Z56772132

Godoy, A.S., Noske, G.D., Fairhead, M., Lithgo, R.M., Koekemoer, L., Aschenbrenner, J.C., Balcomb, B.H., Marples, P.G., Ni, X., Tomlinson, C.W.E., Wild, C., Mesquita, N.C.M.R., Oliva, G., Fearon, D., Walsh, M.A., von Delft, F.

To be published.

Macromolecule Content

Total Structure Weight: 50.15 kDa
Atom Count: 4,003
Modeled Residue Count: 435
Deposited Residue Count: 435
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q32ZE1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YG9 (Subject of Investigation/LOI) Query on YG9 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	(5R)-5-[2-(4-methoxyphenyl)ethyl]-5-methylimidazolidine-2,4-dione C₁₃ H₁₆ N₂ O₃ HYRDVXQOZUFAFW-CYBMUJFWSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.41 Å
R-Value Free: 0.206 (Depositor), 0.221 (DCC)
R-Value Work: 0.168 (Depositor)
R-Value Observed: 0.170 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.97	α = 90
b = 68.68	β = 92.42
c = 57.15	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-12-20

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--
Sao Paulo Research Foundation (FAPESP)	Brazil	--