9OB9 | pdb_00009ob9

Crystal structure of nucleoside-diphosphate kinase from Cryptosporidium parvum in complex with with ADP and CTP

PDB DOI: https://doi.org/10.2210/pdb9OB9/pdb

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

Deposited: 2025-04-22 Released: 2025-04-30
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: 1.60 Å
R-Value Free:
0.178 (Depositor), 0.192 (DCC)
R-Value Work:
0.150 (Depositor), 0.163 (DCC)
R-Value Observed:
0.151 (Depositor)

Starting Model: in silico
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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 nucleoside-diphosphate kinase Cryptosporidium parvum in complex with ADP and CTP

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

To be published.

Macromolecule Content

Total Structure Weight: 55.64 kDa
Atom Count: 4,113
Modeled Residue Count: 447
Deposited Residue Count: 468
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	156	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CTP (Subject of Investigation/LOI) Query on CTP Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain J [auth C] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain J [auth C] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain J [auth C] mmCIF format, chain D [auth A]	D [auth A], G [auth B], J [auth C]	CYTIDINE-5'-TRIPHOSPHATE C₉ H₁₆ N₃ O₁₄ P₃ PCDQPRRSZKQHHS-XVFCMESISA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Focus chain J [auth C] Interactions & Density Focus chain D [auth A] Focus chain G [auth B] Focus chain J [auth C]
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C]	E [auth A], H [auth B], K [auth C]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth C] SDF format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain L [auth C] MOL2 format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain L [auth C] mmCIF format, chain I [auth B]	F [auth A], I [auth B], L [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.178 (Depositor), 0.192 (DCC)
R-Value Work: 0.150 (Depositor), 0.163 (DCC)
R-Value Observed: 0.151 (Depositor)

Diffraction Data:

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.784	α = 90
b = 69.784	β = 90
c = 315.704	γ = 120

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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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-04-30

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