4QOX

Crystal Structure of CDPK4 from Plasmodium Falciparum, PF3D7_0717500

PDB DOI: https://doi.org/10.2210/pdb4QOX/pdb

Classification: TRANSFERASE
Organism(s): Plasmodium falciparum 3D7
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2014-06-20 Released: 2014-09-03
Deposition Author(s): Wernimont, A.K., Walker, J.R., Hutchinson, A., Seitova, A., He, H., Loppnau, P., Neculai, M., Amani, M., Lin, Y.H., Ravichandran, M., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Hui, R., Lovato, D.V., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.266
R-Value Work: 0.203
R-Value Observed: 0.206

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 CDPK4 from Plasmodium Falciparum, PF3D7_0717500

Wernimont, A.K., Walker, J.R., Hutchinson, A., Seitova, A., He, H., Loppnau, P., Neculai, M., Amani, M., Lin, Y.H., Ravichandran, M., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Hui, R., Lovato, D.V.

To be published.

Macromolecule Content

Total Structure Weight: 62.52 kDa
Atom Count: 3,701
Modelled Residue Count: 462
Deposited Residue Count: 537
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium-dependent protein kinase 4	A	537	Plasmodium falciparum 3D7	Mutation(s): 0 Gene Names: CDPK4, CPK4, PF07_0072 EC: 2.7.11.1
UniProt
Find proteins for Q8IBS5 (Plasmodium falciparum (isolate 3D7)) Explore Q8IBS5 Go to UniProtKB: Q8IBS5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8IBS5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DXR Query on DXR Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	3-(3-bromobenzyl)-1-tert-butyl-1H-pyrazolo[3,4-d]pyrimidin-4-amine C₁₆ H₁₈ Br N₅ FTICVONBLRGQJW-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 2.75 Å
R-Value Free: 0.266
R-Value Work: 0.203
R-Value Observed: 0.206
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.289	α = 90
b = 75.967	β = 90
c = 92.688	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
DENZO	data reduction
SCALEPACK	data scaling
HKL-3000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-09-03

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2014-09-03
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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4QOX

Crystal Structure of CDPK4 from Plasmodium Falciparum, PF3D7_0717500

Crystal Structure of CDPK4 from Plasmodium Falciparum, PF3D7_0717500

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)