9ZOG | pdb_00009zog

Crystal structure of nucleoside-diphosphate kinase Cryptosporidium parvum (Apo, hexamer)

PDB DOI: https://doi.org/10.2210/pdb9ZOG/pdb

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

Deposited: 2025-12-15 Released: 2025-12-24
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: 1.48 Å
R-Value Free:
0.161 (Depositor), 0.169 (DCC)
R-Value Work:
0.128 (Depositor), 0.141 (DCC)
R-Value Observed:
0.130 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of nucleoside-diphosphate kinase Cryptosporidium parvum (Apo, hexamer)

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

To be published.

Macromolecule Content

Total Structure Weight: 107.12 kDa
Atom Count: 8,352
Modeled Residue Count: 902
Deposited Residue Count: 942
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
nucleoside-diphosphate kinase	A, B, C, D, E A, B, C, D, E, F	157	Cryptosporidium parvum Iowa II	Mutation(s): 0 Gene Names: cgd4_1940 EC: 2.7.4.6
UniProt
Find proteins for Q5CR64 (Cryptosporidium parvum (strain Iowa II)) Explore Q5CR64 Go to UniProtKB: Q5CR64
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5CR64
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain N [auth E] SDF format, chain Q [auth F] SDF format, chain P [auth E] SDF format, chain O [auth E] SDF format, chain M [auth E] SDF format, chain K [auth D] SDF format, chain J [auth C] SDF format, chain I [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain N [auth E] MOL2 format, chain Q [auth F] MOL2 format, chain P [auth E] MOL2 format, chain O [auth E] MOL2 format, chain M [auth E] MOL2 format, chain K [auth D] MOL2 format, chain J [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain N [auth E] mmCIF format, chain Q [auth F] mmCIF format, chain P [auth E] mmCIF format, chain O [auth E] mmCIF format, chain M [auth E] mmCIF format, chain K [auth D] mmCIF format, chain J [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth B] J [auth C] K [auth D] G [auth A], H [auth A], I [auth B], J [auth C], K [auth D], M [auth E], N [auth E], O [auth E], P [auth E], Q [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain M [auth E] Focus chain N [auth E] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain M [auth E] Focus chain N [auth E] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth F]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain L [auth D] MOL2 format, chain L [auth D] mmCIF format, chain L [auth D]	L [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth D] Interactions & Density Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free: 0.161 (Depositor), 0.169 (DCC)
R-Value Work: 0.128 (Depositor), 0.141 (DCC)
R-Value Observed: 0.130 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.963	α = 90
b = 70.646	β = 90
c = 197.623	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-24

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