7M1V | pdb_00007m1v

Structure of Zika virus NS2b-NS3 protease mutant binding the compound NSC86314 in the super-open conformation

PDB DOI: https://doi.org/10.2210/pdb7M1V/pdb

Classification: VIRAL PROTEIN
Organism(s): Zika virus
Expression System: Escherichia coli #1/H766
Mutation(s): No

Deposited: 2021-03-15 Released: 2021-04-21
Deposition Author(s): Aleshin, A.E., Shiryaev, S.A., Liddington, R.C.
Funding Organization(s): National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.189 (Depositor), 0.196 (DCC)
R-Value Work:
0.160 (Depositor), 0.173 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

To be provided

Aleshin, A.E., Shiryaev, S.A., Liddington, R.C.

To be published.

Macromolecule Content

Total Structure Weight: 47.21 kDa
Atom Count: 2,936
Modeled Residue Count: 329
Deposited Residue Count: 442
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Core protein	A, B	221	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 A0A024B7W1 (Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013)) Explore A0A024B7W1 Go to UniProtKB: A0A024B7W1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A024B7W1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YO1 (Subject of Investigation/LOI) Query on YO1 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	4-(2-{2,4-diamino-5-[2-(4-{[(2E)-1,3-thiazolidin-2-ylidene]sulfamoyl}phenyl)hydrazinyl]phenyl}hydrazinyl)-N-[(2S)-1,3-thiazolidin-2-yl]benzene-1-sulfonamide C₂₄ H₂₀ N₁₀ O₄ S₄ BZLWMRWTRRMORD-JWTBXLROSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
DMS Query on DMS 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]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B], H [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B] Focus chain H [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.189 (Depositor), 0.196 (DCC)
R-Value Work: 0.160 (Depositor), 0.173 (DCC)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.81	α = 98.88
b = 42.637	β = 92.11
c = 46.296	γ = 90.41

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-04-21

Deposition Author(s):

Aleshin, A.E.

Shiryaev, S.A.

Liddington, R.C.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)	United States	5R21AI134581

Revision History (Full details and data files)

Version 1.0: 2021-04-21
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-30
Changes: Structure summary