5T6A | pdb_00005t6a

Crystal Structure of TgCDPK1 from toxoplasma gondii complexed with 5GA

PDB DOI: https://doi.org/10.2210/pdb5T6A/pdb
Entry: 5T6A supersedes: 5DVU

Classification: TRANSFERASE
Organism(s): Toxoplasma gondii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-09-01 Released: 2016-11-02
Deposition Author(s): Jiang, D.Q., Tempel, W., Loppnau, P., Walker, J.R., Graslund, S., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Hui, R., Lovato, D.V., Osman, K.T., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.240 (Depositor), 0.247 (DCC)
R-Value Work:
0.203 (Depositor), 0.213 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of TgCDPK1 from toxoplasma gondii complexed with SGC-1-9

Jiang, D.Q., Tempel, W., Loppnau, P., Walker, J.R., Graslund, S., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Hui, R., Lovato, D.V., Osman, K.T., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 59.89 kDa
Atom Count: 3,432
Modeled Residue Count: 431
Deposited Residue Count: 525
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	525	Toxoplasma gondii	Mutation(s): 0 Gene Names: CDPK1 EC: 2.7.11.1
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5GA Query on 5GA 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-(3-chloro-4-fluorophenyl)-5-(1,5-naphthyridin-2-yl)-1,3-thiazol-2-amine C₁₇ H₁₀ Cl F N₄ S QPTHMBUJLWRYEC-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: 2.05 Å
R-Value Free: 0.240 (Depositor), 0.247 (DCC)
R-Value Work: 0.203 (Depositor), 0.213 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.757	α = 90
b = 72.175	β = 97.61
c = 66.142	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
PDB_EXTRACT	data extraction
Aimless	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-11-02

Deposition Author(s):

Structural Genomics Consortium (SGC)

This entry supersedes: 5DVU

Revision History (Full details and data files)

Version 1.0: 2016-11-02
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description