7ZUM

Crystal Structure of Unlinked NS2B-NS3 Protease from Zika Virus in Complex with Inhibitor MI-2130

• PDB DOI: https://doi.org/10.2210/pdb7ZUM/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Zika virus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-05-12 Released: 2023-03-22 
• Deposition Author(s): Huber, S., Steinmetzer, T.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.204 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Literature

Crystal Structure of Unlinked NS2B-NS3 Protease from Zika Virus in Complex with Inhibitor MI-2130

Huber, S., Braun, N., Steinmetzer, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 25.69 kDa 
• Atom Count: 1,581 
• Modelled Residue Count: 194 
• Deposited Residue Count: 231 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine protease subunit NS2B	A	53	Zika virus	Mutation(s): 0
UniProt
Find proteins for Q32ZE1 (Zika virus) Explore Q32ZE1  Go to UniProtKB:  Q32ZE1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine protease NS3	B	178	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JN9 (Subject of Investigation/LOI)	C [auth B]	1-[(5R,8R,15S,18S)-15-(4-azanylbutyl)-5-(cyclohexylmethyl)-18-(1H-indol-3-ylmethyl)-4,7,14,17,20-pentakis(oxidanylidene)-3,6,13,16,19-pentazabicyclo[20.3.1]hexacosa-1(25),22(26),23-trien-8-yl]guanidine C42 H60 N10 O5 FYPRNDPBQZMJGG-NZKHRDNMSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.204 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.343	α = 90
b = 60.623	β = 90
c = 80.889	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-03-22 
Deposition Author(s): Huber, S., Steinmetzer, T.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-03-22
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Data collection, Refinement description