7I28 | pdb_00007i28

Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z45527714 (DNV2_NS5A-x0153)

PDB DOI: https://doi.org/10.2210/pdb7I28/pdb
Deposition Group: G_1002341 (changed state) | Explore G_1002341

Classification: VIRAL PROTEIN
Organism(s): dengue virus type 2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-03-06 Released: 2025-04-02
Deposition Author(s): Aschenbrenner, J.C., Saini, M., Chopra, A., Marples, P.G., Balcomb, B.H., Lithgo, R.M., Fearon, D., von Delft, F., Ruiz, F.X., Arnold, E.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free:
0.250 (Depositor)
R-Value Work:
0.217 (Depositor)
R-Value Observed:
0.219 (Depositor)

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This is version 1.0 of the entry. See complete history.

Literature

Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2

Aschenbrenner, J.C., Saini, M., Chopra, A., Marples, P.G., Balcomb, B.H., Lithgo, R.M., Fearon, D., von Delft, F., Ruiz, F.X., Arnold, E.

To be published.

Macromolecule Content

Total Structure Weight: 75.22 kDa
Atom Count: 5,083
Modeled Residue Count: 571
Deposited Residue Count: 637
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NS5 RNA-dependent RNA polymerase	A	637	dengue virus type 2	Mutation(s): 0
UniProt
Find proteins for Q91H74 (Dengue virus type 2) Explore Q91H74 Go to UniProtKB: Q91H74
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q91H74
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
X0S (Subject of Investigation/LOI) Query on X0S Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A]	K [auth A], L [auth A]	2-chloro-N-methylbenzene-1-sulfonamide C₇ H₈ Cl N O₂ S OSFAUZAAZLLTSW-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain D [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain G [auth A] MOL2 format, chain J [auth A] MOL2 format, chain G [auth A] mmCIF format, chain J [auth A] mmCIF format, chain G [auth A]	G [auth A], J [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain H [auth A] Focus chain I [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain M [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free: 0.250 (Depositor)
R-Value Work: 0.217 (Depositor)
R-Value Observed: 0.219 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.558	α = 90
b = 117.169	β = 90
c = 148.292	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-04-02

Deposition Author(s):

Aschenbrenner, J.C.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U19AI171292

Revision History (Full details and data files)

Version 1.0: 2025-04-02
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.