9EF8 | pdb_00009ef8

Crystal structure of Cryptosporidium parvum N-myristoyltransferase with bound myristoyl-CoA and inhibitor 20084

PDB DOI: https://doi.org/10.2210/pdb9EF8/pdb

Classification: TRANSFERASE/INHIBITOR
Organism(s): Cryptosporidium parvum Iowa II
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2024-11-19 Released: 2025-11-26
Deposition Author(s): Fenwick, M.K., Staker, B.L., Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free:
0.231 (Depositor), 0.231 (DCC)
R-Value Work:
0.180 (Depositor), 0.180 (DCC)
R-Value Observed:
0.182 (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 Cryptosporidium parvum N-myristoyltransferase with bound myristoyl-CoA and inhibitor 20084

Staker, B.L., Fan, E.

To be published.

Macromolecule Content

Total Structure Weight: 52.35 kDa
Atom Count: 4,109
Modeled Residue Count: 427
Deposited Residue Count: 431
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycylpeptide N-tetradecanoyltransferase	A	431	Cryptosporidium parvum Iowa II	Mutation(s): 0 Gene Names: cgd3_320 EC: 2.3.1.97
UniProt
Find proteins for Q5CV46 (Cryptosporidium parvum (strain Iowa II)) Explore Q5CV46 Go to UniProtKB: Q5CV46
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5CV46
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MYA (Subject of Investigation/LOI) Query on MYA 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]	TETRADECANOYL-COA C₃₅ H₆₂ N₇ O₁₇ P₃ S DUAFKXOFBZQTQE-QSGBVPJFSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
A1BHR (Subject of Investigation/LOI) Query on A1BHR 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]	2-[1-(1,4-diazepan-1-yl)naphthalen-2-yl]-N-(4,5-dimethyl-1,3-thiazol-2-yl)-3-oxo-2,3-dihydro-1H-isoindole-4-carboxamide C₂₉ H₂₉ N₅ O₂ S GXYJKXIGRWIEKQ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A], F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free: 0.231 (Depositor), 0.231 (DCC)
R-Value Work: 0.180 (Depositor), 0.180 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.961	α = 90
b = 68.664	β = 90
c = 149.991	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHASER	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-26

Deposition Author(s):

Fenwick, M.K.

Staker, B.L.

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	R01 AI155536
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	6R21 AI137815-02