9RM4 | pdb_00009rm4

Crystal Structure of ZIKV NS2B-NS3 protease in complex with ASAP-0015373

• PDB DOI: https://doi.org/10.2210/pdb9RM4/pdb

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


• Deposited: 2025-06-17 Released: 2025-07-23 
• Deposition Author(s): Ni, X., Marples, P.G., Godoy, A.S., Koekemoer, L., Aschenbrenner, J.C., Balcomb, B.H., Fairhead, M., Lithgo, R.M., Lee, A., Kenton, N., Thompson, W., Tomlinson, C.W.E., Wild, C., Winokan, M., Williams, E.P., Fearon, D., von Delft, F.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.278 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.214 (DCC) 

Starting Model: experimental

Literature

Crystal Structure of ZIKV NS2B-NS3 protease in complex with ASAP-0015373

Ni, X., Marples, P.G., Godoy, A.S., Koekemoer, L., Aschenbrenner, J.C., Balcomb, B.H., Fairhead, M., Lithgo, R.M., Lee, A., Kenton, N., Thompson, W., Tomlinson, C.W.E., Wild, C., Winokan, M., Williams, E.P., 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: 46.75 kDa 
• Atom Count: 1,529 
• Modeled Residue Count: 191 
• Deposited Residue Count: 428 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine protease subunit NS2B,Serine protease NS3	A [auth AAA], B [auth BBB]	214	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1JHM (Subject of Investigation/LOI)	C [auth BBB]	~{N}-[3-chloranyl-5-[(2-methyl-1-oxidanyl-propan-2-yl)carbamoyl]phenyl]-5-[(dimethylamino)methyl]-1~{H}-pyrrole-2-carboxamide C19 H25 Cl N4 O3 ISSINQXJUZDLQL-UHFFFAOYSA-N
NA	D [auth BBB]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.278 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.214 (DCC) 

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.42	α = 90
b = 42.42	β = 90
c = 215.96	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-23 
Deposition Author(s): Ni, X., Marples, P.G., Godoy, A.S., Koekemoer, L., Aschenbrenner, J.C., Balcomb, B.H., Fairhead, M., Lithgo, R.M., Lee, A., Kenton, N., Thompson, W., Tomlinson, C.W.E., Wild, C., Winokan, M., Williams, E.P., Fearon, D., 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	--

Revision History  

• Version 1.0: 2025-07-23
  Type: Initial release