4IFG | pdb_00004ifg

Crystal structure of TgCDPK1 with inhibitor bound

PDB DOI: https://doi.org/10.2210/pdb4IFG/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Toxoplasma gondii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-12-14 Released: 2014-04-16
Deposition Author(s): El Bakkouri, M., Tempel, W., Crandall, I., Massad, T., Loppnau, P., Graslund, S., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Kain, K., Hui, R., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free:
0.266 (Depositor), 0.264 (DCC)
R-Value Work:
0.210 (Depositor), 0.208 (DCC)
R-Value Observed:
0.213 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of TgCDPK1 with inhibitor bound

El Bakkouri, M., Tempel, W., Crandall, I., Massad, T., Loppnau, P., Graslund, S., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Kain, K., Hui, R., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 57.77 kDa
Atom Count: 3,713
Modeled Residue Count: 452
Deposited Residue Count: 507
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calmodulin-domain protein kinase 1	A	507	Toxoplasma gondii	Mutation(s): 0 Gene Names: CDPK1, TGGT1_059880, TGVEG_042030 EC: 2.7.11.17 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt
Find proteins for Q9BJF5 (Toxoplasma gondii) Explore Q9BJF5 Go to UniProtKB: Q9BJF5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BJF5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1E8 Query on 1E8 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]	1-{(3R)-3-[4-amino-3-(4-phenoxyphenyl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl]piperidin-1-yl}prop-2-en-1-one C₂₅ H₂₄ N₆ O₂ XYFPWWZEPKGCCK-GOSISDBHSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
UNX Query on UNX 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]	UNKNOWN ATOM OR ION X		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free: 0.266 (Depositor), 0.264 (DCC)
R-Value Work: 0.210 (Depositor), 0.208 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.397	α = 90
b = 72.778	β = 101.66
c = 67.085	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
JBluIce-EPICS	data collection

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-04-16

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2014-04-16
Type: Initial release
Version 1.1: 2015-03-11
Changes: Non-polymer description
Version 1.2: 2017-11-15
Changes: Refinement description
Version 1.3: 2024-02-28
Changes: Data collection, Database references, Derived calculations, Structure summary