4YZB | pdb_00004yzb

CDPK1 from Eimeria tenella in complex with inhibitor UW1521

PDB DOI: https://doi.org/10.2210/pdb4YZB/pdb

Classification: Transferase/Transferase Inhibitor
Organism(s): Eimeria tenella
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2015-03-24 Released: 2016-04-06
Deposition Author(s): Merritt, E.A.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.284 (Depositor), 0.280 (DCC)
R-Value Work:
0.242 (Depositor), 0.245 (DCC)
R-Value Observed:
0.244 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

CDPK is a druggable target in the apicomplexan parasite Eimeria

Ojo, K.K., Vidadala, R., Maly, D.J., Van Voorhis, W.C., Merritt, E.A.

To be published.

Macromolecule Content

Total Structure Weight: 112.46 kDa
Atom Count: 7,475
Modeled Residue Count: 930
Deposited Residue Count: 982
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calmodulin-like domain protein kinase	A, B	491	Eimeria tenella	Mutation(s): 1 EC: 2.7.11.1
UniProt
Find proteins for Q3HNM4 (Eimeria tenella) Explore Q3HNM4 Go to UniProtKB: Q3HNM4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3HNM4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BK8 Query on BK8 Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A]	G [auth A], L [auth B]	4-(6-ethoxynaphthalen-2-yl)-6-(piperazin-1-ylmethyl)-2H-indazol-3-amine C₂₄ H₂₇ N₅ O ZBGMTSWSDGHDMV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] H [auth B] C [auth A], D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.284 (Depositor), 0.280 (DCC)
R-Value Work: 0.242 (Depositor), 0.245 (DCC)
R-Value Observed: 0.244 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.259	α = 90
b = 97.95	β = 94.56
c = 89.93	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-04-06

Deposition Author(s):

Merritt, E.A.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI089441

Revision History (Full details and data files)

Version 1.0: 2016-04-06
Type: Initial release
Version 1.1: 2017-09-20
Changes: Author supporting evidence, Derived calculations
Version 1.2: 2019-12-11
Changes: Author supporting evidence
Version 1.3: 2023-09-27
Changes: Data collection, Database references, Refinement description

4YZB | pdb_00004yzb

CDPK1 from Eimeria tenella in complex with inhibitor UW1521

Literature

CDPK is a druggable target in the apicomplexan parasite Eimeria

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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