5RHT | pdb_00005rht

PanDDA analysis group deposition -- Crystal Structure of Zika virus NS3 Helicase in complex with Z291279160

• PDB DOI: https://doi.org/10.2210/pdb5RHT/pdb
• Deposition Group: G_1002158 (changed state) | Explore  G_1002158  

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


• Deposited: 2020-05-25 Released: 2020-06-10 
• Deposition Author(s): Godoy, A.S., Mesquita, N.C.M.R., Oliva, G.
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 
  0.220 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

PanDDA analysis group deposition

Godoy, A.S., Mesquita, N.C.M.R., Oliva, G.

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: 49.56 kDa 
• Atom Count: 3,918 
• Modeled Residue Count: 435 
• Deposited Residue Count: 435 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NS3 Helicase	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
LV4 (Subject of Investigation/LOI)	F [auth A]	1-[2-(trifluoromethyloxy)phenyl]thiourea C8 H7 F3 N2 O S HYKOSRYWIURWQI-UHFFFAOYSA-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: 1.63 Å
• R-Value Free:  0.220 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.42	α = 90
b = 68.934	β = 92.32
c = 57.182	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-06-10 
Deposition Author(s): Godoy, A.S., Mesquita, N.C.M.R., Oliva, G.

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Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2013/07600-3

Revision History  

• Version 1.0: 2020-06-10
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references
• Version 1.2: 2026-02-18
  Changes: Refinement description, Structure summary