8V7U

PanDDA analysis -- Crystal Structure of Zika virus NS3 Helicase in complex with Z729726784

• PDB DOI: https://doi.org/10.2210/pdb8V7U/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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.215 
• R-Value Work: 0.186 
• R-Value Observed: 0.187 

Literature

PanDDA analysis -- Crystal Structure of Zika virus NS3 Helicase in complex with Z729726784

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 50.04 kDa 
• Atom Count: 3,832 
• Modelled Residue Count: 435 
• Deposited Residue Count: 435 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YDU (Subject of Investigation/LOI)	M [auth A]	2-cyclopentyl-N-(3-methyl-1,2,4-oxadiazol-5-yl)acetamide C10 H15 N3 O2 BXPGKHXJBBUYFC-UHFFFAOYSA-N
PO4	K [auth A], L [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
DMS	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO	J [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.215 
• R-Value Work: 0.186 
• R-Value Observed: 0.187 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.6	α = 90
b = 69.55	β = 92.13
c = 56.94	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 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.

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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	--

Revision History  

• Version 1.0: 2023-12-20
  Type: Initial release
  
• Version 1.1: 2024-03-13
  Changes: Source and taxonomy