5IF8 | pdb_00005if8

Crystal structure of polymerase acid protein (PA) from Influenza A virus, WILSON-SMITH/1933 (H1N1) bound to fragment hit EBSI-2643 5-[(4-chlorophenyl)methyl]-1,3,4-oxadiazol-2-amine

PDB DOI: https://doi.org/10.2210/pdb5IF8/pdb

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

Deposited: 2016-02-25 Released: 2017-02-22
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.232 (Depositor), 0.233 (DCC)
R-Value Work:
0.182 (Depositor), 0.183 (DCC)
R-Value Observed:
0.185 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Fragment screening by STD NMR identifies novel site binders against influenza A virus polymerase PA

Pierce, P., Muruthi, M.M., Abendroth, J., Moen, S.O., Begley, D.W., Davies, D.R., Marathias, V.M., Staker, B.L., Myler, P.J., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 53.57 kDa
Atom Count: 3,280
Modeled Residue Count: 402
Deposited Residue Count: 464
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polymerase acidic protein	A	464	Influenza A virus (A/Wilson-Smith/1933(H1N1))	Mutation(s): 0 Gene Names: PA EC: 3.1
UniProt
Find proteins for P15659 (Influenza A virus (strain A/Wilson-Smith/1933 H1N1)) Explore P15659 Go to UniProtKB: P15659
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P15659
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6AX Query on 6AX Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	5-[(4-chlorophenyl)methyl]-1,3,4-oxadiazol-2-amine C₉ H₈ Cl N₃ O CSYAPQQQRVPGKN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
DMS Query on DMS 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]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
EDO Query on EDO 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]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CL Query on CL 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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.232 (Depositor), 0.233 (DCC)
R-Value Work: 0.182 (Depositor), 0.183 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.78	α = 90
b = 68.78	β = 90
c = 396.1	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2017-02-22

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2017-02-22
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, Database references

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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.