5CXR | pdb_00005cxr

Influenza endonuclease complexed with 4-bromopyrazole

PDB DOI: https://doi.org/10.2210/pdb5CXR/pdb

Classification: TRANSCRIPTION
Organism(s): Influenza A virus (A/California/02/2010(H1N1))
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-07-29 Released: 2015-12-30
Deposition Author(s): Bauman, J.D., Arnold, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.198 (Depositor), 0.200 (DCC)
R-Value Work:
0.174 (Depositor), 0.177 (DCC)
R-Value Observed:
0.175 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Rapid experimental SAD phasing and hot-spot identification with halogenated fragments.

Bauman, J.D., Harrison, J.J., Arnold, E.

(2016) IUCrJ 3: 51-60

PubMed: 26870381 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2052252515021259
Primary Citation Related Structures:
5CXR, 5CYQ

PubMed Abstract:
Through X-ray crystallographic fragment screening, 4-bromopyrazole was discovered to be a 'magic bullet' that is capable of binding at many of the ligand 'hot spots' found in HIV-1 reverse transcriptase (RT). The binding locations can be in pockets that are 'hidden' in the unliganded crystal form, allowing rapid identification of these sites for in silico screening. In addition to hot-spot identification, this ubiquitous yet specific binding provides an avenue for X-ray crystallographic phase determination, which can be a significant bottleneck in the determination of the structures of novel proteins. The anomalous signal from 4-bromopyrazole or 4-iodopyrazole was sufficient to determine the structures of three proteins (HIV-1 RT, influenza A endonuclease and proteinase K) by single-wavelength anomalous dispersion (SAD) from single crystals. Both compounds are inexpensive, readily available, safe and very soluble in DMSO or water, allowing efficient soaking into crystals.

Organizational Affiliation

Center for Advanced Biotechnology and Medicine, Department of Chemistry and Chemical Biology, Rutgers University , 679 Hoes Lane, Piscataway, NJ 08854, USA.

Macromolecule Content

Total Structure Weight: 25.62 kDa
Atom Count: 1,853
Modeled Residue Count: 201
Deposited Residue Count: 209
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
endonuclease	A	209	Influenza A virus (A/California/02/2010(H1N1))	Mutation(s): 0 Gene Names: PA EC: 3.1
UniProt
Find proteins for M9QLS3 (Influenza A virus) Explore M9QLS3 Go to UniProtKB: M9QLS3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	M9QLS3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BYZ Query on BYZ Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	4-bromo-1H-pyrazole C₃ H₃ Br N₂ WVGCPEDBFHEHEZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [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]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.198 (Depositor), 0.200 (DCC)
R-Value Work: 0.174 (Depositor), 0.177 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.905	α = 90
b = 102.451	β = 90
c = 66.062	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-12-30

Deposition Author(s):

Bauman, J.D.

Arnold, E.

Revision History (Full details and data files)

Version 1.0: 2015-12-30
Type: Initial release
Version 1.1: 2018-04-18
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.2: 2024-03-06
Changes: Data collection, Database references, Derived calculations, Structure summary