3MES

Crystal structure of choline kinase from Cryptosporidium parvum Iowa II, cgd3_2030

PDB DOI: https://doi.org/10.2210/pdb3MES/pdb

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

Deposited: 2010-03-31 Released: 2010-04-07
Deposition Author(s): Qiu, W., Wernimont, A., Hills, T., Lew, J., Artz, J.D., Xiao, T., Allali-Hassani, A., Vedadi, M., Kozieradzki, I., Cossar, D., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Hui, R., Ma, D., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.291
R-Value Work: 0.245
R-Value Observed: 0.247

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of choline kinase from Cryptosporidium parvum Iowa II, cgd3_2030

Qiu, W., Wernimont, A., Hills, T., Lew, J., Artz, J.D., Xiao, T., Allali-Hassani, A., Vedadi, M., Kozieradzki, I., Cossar, D., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Hui, R., Ma, D.

To be published.

Macromolecule Content

Total Structure Weight: 101.19 kDa
Atom Count: 6,326
Modelled Residue Count: 715
Deposited Residue Count: 848
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Choline kinase	A, B	424	Cryptosporidium parvum Iowa II	Mutation(s): 0 Gene Names: cgd3_2030
UniProt
Find proteins for Q5CUP2 (Cryptosporidium parvum (strain Iowa II)) Explore Q5CUP2 Go to UniProtKB: Q5CUP2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5CUP2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B]	C [auth A], I [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
DME Query on DME Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B]	E [auth A], K [auth B]	DECAMETHONIUM ION C₁₆ H₃₈ N₂ MTCUAOILFDZKCO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain K [auth B]
PT3 Query on PT3 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B]	F [auth A], L [auth B]	N-PROPYL-TARTRAMIC ACID C₇ H₁₃ N O₅ LNEZKQHJUNIZIS-RFZPGFLSSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain L [auth B]
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		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 D [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain M [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth B]	D [auth A], H [auth A], J [auth B], M [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain M [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.291
R-Value Work: 0.245
R-Value Observed: 0.247
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.091	α = 90
b = 67.957	β = 116.54
c = 92.109	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
BALBES	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-04-07

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2010-04-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description