3TG6

Crystal Structure of Influenza A Virus nucleoprotein with Ligand

PDB DOI: https://doi.org/10.2210/pdb3TG6/pdb

Classification: VIRAL PROTEIN/INHIBITOR
Organism(s): Influenza A virus (A/Wilson-Smith/1933(H1N1))
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-08-17 Released: 2012-08-29
Deposition Author(s): Pearce, B.C., Lewis, H.A., McDonnell, P.A., Steinbacher, S., Kiefersauer, R., Mortl, M., Maskos, K., Edavettal, S., Baldwin, E.T., Langley, D.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.296
R-Value Work: 0.233
R-Value Observed: 0.235

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Biophysical and Structural Characterization of a Novel Class of Influenza Virus Inhibitors

Edavettal, S.C., Pearce, B.C., Lewis, H.A., Schneeweis, L., Deminie, C., Discotto, L., Carpenter, B., Yanchunas, J., Langley, D.R., Metzler, W., Gao, M., Poss, M.A., Maskos, K., Mortl, M., Keifersauer, R., Steinbacher, S., Healy, M., Phillip, T., Zoeckler, M., Schartman, R., McAuliffe, B., Minassian, B.F., Shi, S., Zhu, S., Pendri, A., Li, G., Sinz, M., Meanwell, N.A., Krystal, M., Gerritz, S.W., Cianci, C., Baldwin, B.T., Bryson, J.W., McDonnell, P.A.

To be published.

Macromolecule Content

Total Structure Weight: 114.54 kDa
Atom Count: 6,302
Modelled Residue Count: 853
Deposited Residue Count: 998
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleocapsid protein	A, B	499	Influenza A virus (A/Wilson-Smith/1933(H1N1))	Mutation(s): 0 Gene Names: NP
UniProt
Find proteins for Q1K9H2 (Influenza A virus (strain A/Wilson-Smith/1933 H1N1)) Explore Q1K9H2 Go to UniProtKB: Q1K9H2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q1K9H2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0MM Query on 0MM Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	[4-(2-chloro-4-nitrophenyl)piperazin-1-yl][3-(2-chloropyridin-3-yl)-5-methyl-1,2-oxazol-4-yl]methanone C₂₀ H₁₇ Cl₂ N₅ O₄ OVZFTYKFOMVVNQ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.296
R-Value Work: 0.233
R-Value Observed: 0.235
Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.692	α = 90
b = 146.692	β = 90
c = 146.692	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-08-29

Deposition Author(s):

McDonnell, P.A.

Steinbacher, S.

Kiefersauer, R.

Revision History (Full details and data files)

Version 1.0: 2012-08-29
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.