9OAK | pdb_00009oak

Crystal structure of nucleoside-diphosphate kinase from Cryptosporidium parvum in complex with cytidine-5'-diphosphate and cytidine-5'-triphosphate

• PDB DOI: https://doi.org/10.2210/pdb9OAK/pdb

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


• Deposited: 2025-04-21 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: 1.61 Å
• R-Value Free: 
  0.172 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.145 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.146 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of nucleoside-diphosphate kinase Cryptosporidium parvum in complex with cytidine-5'-diphosphate and cytidine-5'-triphosphate

Liu, L., Lovell, S., Battaile, K.P.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 54.01 kDa 
• Atom Count: 4,103 
• Modeled Residue Count: 448 
• Deposited Residue Count: 469 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CTP (Subject of Investigation/LOI)	D [auth A]	CYTIDINE-5'-TRIPHOSPHATE C9 H16 N3 O14 P3 PCDQPRRSZKQHHS-XVFCMESISA-N
CDP (Subject of Investigation/LOI)	F [auth C]	CYTIDINE-5'-DIPHOSPHATE C9 H15 N3 O11 P2 ZWIADYZPOWUWEW-XVFCMESISA-N
MG	E [auth A], G [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HIP	A, B, C	L-PEPTIDE LINKING	C6 H11 N3 O5 P		HIS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free:  0.172 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.145 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.146 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M39OAK

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.734	α = 90
b = 69.734	β = 90
c = 316.121	γ = 120

Software Package:

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

Structure Validation

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

Revision History  

• Version 1.0: 2025-04-30
  Type: Initial release