4QJ1

Co-crystal structure of the catalytic domain of the inosine monophosphate dehydrogenase from Cryptosporidium parvum with inhibitor N109

• PDB DOI: https://doi.org/10.2210/pdb4QJ1/pdb

• Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
• Organism(s): Cryptosporidium parvum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-06-03 Released: 2014-08-06 
• Deposition Author(s): Kim, Y., Makowska-Grzyska, M., Gu, M., Hedstrom, L., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free: 0.258 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 

Literature

Co-crystal structure of the catalytic domain of the inosine monophosphate dehydrogenase from Cryptosporidium parvum with inhibitor N109

Kim, Y., Makowska-Grzyska, M., Gu, M., Hedstrom, L., Anderson, W.F., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 157.25 kDa 
• Atom Count: 10,616 
• Modelled Residue Count: 1,378 
• Deposited Residue Count: 1,444 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inosine-5'-monophosphate dehydrogenase	A, B, C, D	361	Cryptosporidium parvum	Mutation(s): 2  Gene Names: 56k.02, cgd6_20 EC: 1.1.1.205
UniProt
Find proteins for Q8T6T2 (Cryptosporidium parvum) Explore Q8T6T2  Go to UniProtKB:  Q8T6T2

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
N09	F [auth A], H [auth B], I [auth B], N [auth D]	N-(4-chloro-3-methoxyphenyl)-2-(4-oxochromeno[4,3-c]pyrazol-1(4H)-yl)acetamide C19 H14 Cl N3 O4 DJHSRZJOSYWGCG-UHFFFAOYSA-N
IMP	E [auth A], G [auth B], K [auth C], M [auth D]	INOSINIC ACID C10 H13 N4 O8 P GRSZFWQUAKGDAV-KQYNXXCUSA-N
EDO	L [auth C], O [auth D], Q [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACY	J [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
FMT	P [auth D]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
N09	BindingDB:  4QJ1	IC50: 20 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free: 0.258 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/M34QJ1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.412	α = 90
b = 92.337	β = 104.24
c = 91.914	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
MOLREP	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-08-06 
Deposition Author(s): Kim, Y., Makowska-Grzyska, M., Gu, M., Hedstrom, L., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2014-08-06
  Type: Initial release
  
• Version 1.1: 2017-07-26
  Changes: Refinement description, Source and taxonomy
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description