5FET | pdb_00005fet

Crystal Structure of PVX_084705 in presence of Compound 2

PDB DOI: https://doi.org/10.2210/pdb5FET/pdb
Entry: 5FET supersedes: 5F0D

Classification: TRANSFERASE
Organism(s): Plasmodium vivax Sal-1
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2015-12-17 Released: 2016-01-13
Deposition Author(s): Wernimont, A.K., Tempel, W., Walker, J.R., He, H., Seitova, A., Hills, T., Neculai, A.M., Baker, D.A., Flueck, C., Kettleborough, C.A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Hui, R., Hutchinson, A., El Bakkouri, M., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.07 Å
R-Value Free:
0.247 (Depositor), 0.249 (DCC)
R-Value Work:
0.228 (Depositor), 0.227 (DCC)
R-Value Observed:
0.229 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of PVX_084705 in presence of Compound 2

Wernimont, A.K., Tempel, W., Walker, J.R., He, H., Seitova, A., Hills, T., Neculai, A.M., Baker, D.A., Flueck, C., Kettleborough, C.A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Hui, R., Hutchinson, A., El Bakkouri, M.

To be published.

Macromolecule Content

Total Structure Weight: 97.09 kDa
Atom Count: 6,319
Modeled Residue Count: 802
Deposited Residue Count: 847
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cGMP-dependent protein kinase, putative	A	847	Plasmodium vivax Sal-1	Mutation(s): 0 Gene Names: PVX_084705 EC: 2.7.11.12
UniProt
Find proteins for A5K0N4 (Plasmodium vivax (strain Salvador I)) Explore A5K0N4 Go to UniProtKB: A5K0N4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A5K0N4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1TR Query on 1TR 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]	4-[7-[(dimethylamino)methyl]-2-(4-fluorophenyl)imidazo[1,2-a]pyridin-3-yl]pyrimidin-2-amine C₂₀ H₁₉ F N₆ HEPQZLAAWOEYMZ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.07 Å
R-Value Free: 0.247 (Depositor), 0.249 (DCC)
R-Value Work: 0.228 (Depositor), 0.227 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 190.52	α = 90
b = 117.25	β = 94.34
c = 67.42	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data reduction
HKL-2000	data scaling
PHASER	phasing
BUSTER	refinement
DENZO	data reduction
SCALEPACK	data scaling
HKL-3000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-01-13

Deposition Author(s):

Structural Genomics Consortium (SGC)

This entry supersedes: 5F0D

Revision History (Full details and data files)

Version 1.0: 2016-01-13
Type: Initial release
Version 1.1: 2017-11-22
Changes: Advisory, Derived calculations, Refinement description
Version 1.2: 2024-03-06
Changes: Advisory, Data collection, Database references