7HP7 | pdb_00007hp7

PanDDA analysis group deposition -- Crystal Structure of ZIKV NS2B-NS3 protease in complex with ASAP-0014939-001

PDB DOI: https://doi.org/10.2210/pdb7HP7/pdb
Deposition Group: G_1002322 (changed state) | Explore G_1002322

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

Deposited: 2024-11-07 Released: 2025-02-26
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., Chandran, A.V., Walsh, M.A., Fearon, D., von Delft, F.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free:
0.286 (Depositor), 0.288 (DCC)
R-Value Work:
0.227 (Depositor), 0.235 (DCC)
R-Value Observed:
0.230 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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., Lee, A., Kenton, N., 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.

Macromolecule Content

Total Structure Weight: 24.12 kDa
Atom Count: 2,214
Modeled Residue Count: 195
Deposited Residue Count: 214
Unique protein chains: 2

Macromolecules

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q32ZE1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q32ZE1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1BGN (Subject of Investigation/LOI) Query on A1BGN Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	(8S)-7-{[6-methoxy-2-(piperazin-1-yl)pyrimidin-4-yl]methoxy}-5-methyl[1,2,4]triazolo[1,5-a]pyrimidine C₁₆ H₂₀ N₈ O₂ CGSRTOYWSPEOSW-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain G [auth B] MOL2 format, chain I [auth B] MOL2 format, chain G [auth B] mmCIF format, chain I [auth B] mmCIF format, chain G [auth B]	G [auth B], I [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth B] Focus chain I [auth B] Interactions & Density Focus chain G [auth B] Focus chain I [auth B]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain H [auth B] SDF format, chain E [auth B] SDF format, chain D [auth B] SDF format, chain C [auth B] MOL2 format, chain J [auth B] MOL2 format, chain H [auth B] MOL2 format, chain E [auth B] MOL2 format, chain D [auth B] MOL2 format, chain C [auth B] mmCIF format, chain J [auth B] mmCIF format, chain H [auth B] mmCIF format, chain E [auth B] mmCIF format, chain D [auth B] mmCIF format, chain C [auth B]	C [auth B], D [auth B], E [auth B], H [auth B], J [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain H [auth B] Focus chain J [auth B] Interactions & Density Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain H [auth B] Focus chain J [auth B]