7H2B

PanDDA analysis group deposition -- Crystal Structure of ZIKV NS2B-NS3 protease in complex with Z1272517105

PDB DOI: https://doi.org/10.2210/pdb7H2B/pdb
Deposition Group: G_1002289 (changed state) ExploreG_1002289

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

Deposited: 2024-04-03 Released: 2024-05-08
Deposition Author(s): Ni, X., Godoy, A.S., Marples, P.G., Fairhead, M., Balcomb, B.H., Tomlinson, C.W.E., Koekemoer, L., Aschenbrenner, J.C., Lithgo, R.M., Thompson, W., Wild, C., Williams, E.P., Winokan, M., Chandran, A.V., Fearon, D., Walsh, M.A., 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: 1.60 Å
R-Value Free: 0.253
R-Value Work: 0.228
R-Value Observed: 0.229

Starting Model: experimental
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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 of ZIKV NS2B-NS3 protease

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

To be published.

Macromolecule Content

Total Structure Weight: 24.12 kDa
Atom Count: 1,700
Modelled Residue Count: 195
Deposited Residue Count: 214
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q32ZE1
Sequence AnnotationsExpand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q32ZE1
Sequence AnnotationsExpand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1AJ3 (Subject of Investigation/LOI) Query on A1AJ3 Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	{(1S,2S)-1-methyl-2-[(3-methyl-1,2,4-thiadiazol-5-yl)amino]cyclopentyl}methanol C₁₀ H₁₇ N₃ O S OXBOFYWMHPKHNR-WCBMZHEXSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth B] SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain C [auth B] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain C [auth B] mmCIF format, chain D [auth B] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	C [auth B] D [auth B] E [auth B] F [auth B] H [auth B] C [auth B], D [auth B], E [auth B], F [auth B], H [auth B], I [auth B], J [auth B], K [auth B], L [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 F [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]