9MI4 | pdb_00009mi4

Crystal structure of calcium-dependent protein kinase 1 (CDPK1) from Cryptosporidium parvum in complex with inhibitor WIN-3-115

PDB DOI: https://doi.org/10.2210/pdb9MI4/pdb

Classification: TRANSFERASE
Organism(s): Cryptosporidium parvum Iowa II
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-12-12 Released: 2025-12-17
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.94 Å
R-Value Free:
0.248 (Depositor), 0.243 (DCC)
R-Value Work:
0.199 (Depositor), 0.201 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of calcium-dependent protein kinase 1 (CDPK1) from Cryptosporidium parvum in complex with inhibitor WIN-3-115.

Liu, L., Cooper, A., Lovell, S., Battaile, K.P.

To be published.

Macromolecule Content

Total Structure Weight: 57.4 kDa
Atom Count: 3,627
Modeled Residue Count: 456
Deposited Residue Count: 492
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calmodulin-domain protein kinase 1	A	492	Cryptosporidium parvum Iowa II	Mutation(s): 0 Gene Names: cgd3_920 EC: 2.7.11.1
UniProt
Find proteins for A3FQ16 (Cryptosporidium parvum (strain Iowa II)) Explore A3FQ16 Go to UniProtKB: A3FQ16
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A3FQ16
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1BLB (Subject of Investigation/LOI) Query on A1BLB 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]	(6M)-6-(2,4-dichlorophenyl)-8-(2-hydroxyethyl)-2-[3-(methanesulfonyl)anilino]pyrido[2,3-d]pyrimidin-7(8H)-one C₂₂ H₁₈ Cl₂ N₄ O₄ S JNFJRESDJRZKPM-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain B [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain B [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain B [auth A]	B [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain D [auth A] Focus chain E [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.94 Å
R-Value Free: 0.248 (Depositor), 0.243 (DCC)
R-Value Work: 0.199 (Depositor), 0.201 (DCC)
R-Value Observed: 0.202 (Depositor)

Diffraction Data: https://doi.org/10.18430/M39MI4

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.855	α = 90
b = 56.641	β = 103.94
c = 80.397	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-12-17

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00036
National Institutes of Health/Office of the Director	United States	S10OD030394