7I21 | pdb_00007i21

PanDDA analysis group deposition -- Crystal Structure of ZIKV NS2B-NS3 protease in complex with NegAcid3-Am03

• PDB DOI: https://doi.org/10.2210/pdb7I21/pdb
• Deposition Group: G_1002340 (changed state) ExploreG_1002340

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


• Deposited: 2025-02-20 Released: 2025-03-05 
• Deposition Author(s): Ni, X., Marples, P.G., Godoy, A.S., Koekemoer, L., Aschenbrenner, J.C., Balcomb, B.H., Fairhead, M., Lithgo, R.M., Balaji, G., Phelps, J., Thompson, W., Tomlinson, C.W.E., Wild, C., Winokan, M., Williams, E.P., Chandran, A.V., Walsh, M.A., Fearon, D., von Delft, F.
• Funding Organization(s): Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 
  0.305 (Depositor), 0.306 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.249 (DCC) 
• R-Value Observed: 
  0.243 (Depositor) 

Starting Model: experimental

Literature

PanDDA analysis group deposition

Ni, X., Marples, P.G., Godoy, A.S., Koekemoer, L., Aschenbrenner, J.C., Balcomb, B.H., Fairhead, M., Lithgo, R.M., Balaji, G., Phelps, J., Thompson, W., Tomlinson, C.W.E., Wild, C., Winokan, M., Williams, E.P., Chandran, A.V., Walsh, M.A., Fearon, D., von Delft, F.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 24 kDa 
• Atom Count: 1,954 
• Modeled Residue Count: 195 
• Deposited Residue Count: 214 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine protease subunit NS2B	A	46	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	168	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1BXS (Subject of Investigation/LOI)	F [auth B]	1-[(3S)-3-(aminomethyl)pyrrolidin-1-yl]-2-[4-(hydroxymethyl)-2-methylquinolin-8-yl]ethan-1-one C18 H23 N3 O2 LTNTUVLYAZVEDA-ZDUSSCGKSA-N
SO4	G [auth B], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DMS	C [auth B], D [auth B], E [auth B], H [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free:  0.305 (Depositor), 0.306 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.249 (DCC) 
• R-Value Observed: 0.243 (Depositor) 

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.581	α = 90
b = 42.581	β = 90
c = 216.368	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-05 
Deposition Author(s): Ni, X., Marples, P.G., Godoy, A.S., Koekemoer, L., Aschenbrenner, J.C., Balcomb, B.H., Fairhead, M., Lithgo, R.M., Balaji, G., Phelps, J., Thompson, W., Tomlinson, C.W.E., Wild, C., Winokan, M., Williams, E.P., Chandran, A.V., Walsh, M.A., Fearon, D., von Delft, F.

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Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	IC180100021

Revision History  

• Version 1.0: 2025-03-05
  Type: Initial release
  
• Version 1.1: 2025-05-28
  Changes: Structure summary