7G9X

PanDDA analysis group deposition -- Crystal Structure of Zika virus NS3 Helicase in complex with Z905065822

• PDB DOI: https://doi.org/10.2210/pdb7G9X/pdb
• Deposition Group: G_1002270 (changed state) ExploreG_1002270

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


• Deposited: 2023-07-03 Released: 2023-07-26 
• 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: 1.81 Å
• R-Value Free: 0.282 
• R-Value Work: 0.228 
• R-Value Observed: 0.230 

Literature

PanDDA analysis group deposition

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: 49.49 kDa 
• Atom Count: 3,852 
• Modelled Residue Count: 435 
• Deposited Residue Count: 435 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine protease NS3	A	435	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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZV5 (Subject of Investigation/LOI)	F [auth A]	(5R)-1,3,7-triazaspiro[4.5]decane-2,4-dione C7 H11 N3 O2 PLFDWSDBRBNQLQ-SSDOTTSWSA-N
MPD	E [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
PO4	C [auth A], D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.282 
• R-Value Work: 0.228 
• R-Value Observed: 0.230 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.253	α = 90
b = 69.863	β = 91.63
c = 57.336	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-26 
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	U19AI171399
Sao Paulo Research Foundation (FAPESP)	Brazil	2013/07600-3

Revision History  

• Version 1.0: 2023-07-26
  Type: Initial release
  
• Version 1.1: 2024-05-22
  Changes: Data collection