4RV8 | pdb_00004rv8

Co-Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Cryptosporidium parvum and the inhibitor p131

• PDB DOI: https://doi.org/10.2210/pdb4RV8/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Cryptosporidium parvum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-11-25 Released: 2014-12-31 
• Deposition Author(s): Kim, Y., Makowska-Grzyska, M., Gu, M., Kavitha, 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: 2.05 Å
• R-Value Free: 
  0.229 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.187 (Depositor) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Structure of Cryptosporidium IMP dehydrogenase bound to an inhibitor with in vivo antiparasitic activity.

Kim, Y., Makowska-Grzyska, M., Gorla, S.K., Gollapalli, D.R., Cuny, G.D., Joachimiak, A., Hedstrom, L.

(2015) Acta Crystallogr F Struct Biol Commun 71: 531-538

• PubMed: 25945705 
• DOI: https://doi.org/10.1107/S2053230X15000187
• Primary Citation Related Structures: 
  4RV8


• PubMed Abstract: 
  

  Inosine 5'-monophosphate dehydrogenase (IMPDH) is a promising target for the treatment of Cryptosporidium infections. Here, the structure of C. parvum IMPDH (CpIMPDH) in complex with inosine 5'-monophosphate (IMP) and P131, an inhibitor with in vivo anticryptosporidial activity, is reported. P131 contains two aromatic groups, one of which interacts with the hypoxanthine ring of IMP, while the second interacts with the aromatic ring of a tyrosine in the adjacent subunit. In addition, the amine and NO2 moieties bind in hydrated cavities, forming water-mediated hydrogen bonds to the protein. The design of compounds to replace these water molecules is a new strategy for the further optimization of C. parvum inhibitors for both antiparasitic and antibacterial applications.

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Organizational Affiliation: 
• Center for Structural Genomics of Infectious Diseases, Computational Institute, University of Chicago, 5735 S. Ellis Avenue, Chicago, IL 60637, USA.
Department of Biology, Brandeis University, 415 South Street, Waltham, MA 02454, USA.
Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Science and Research Building 2, Houston, TX 77204, USA.

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: 157.93 kDa 
• Atom Count: 10,414 
• Modeled Residue Count: 1,307 
• 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): 0  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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
I13	F [auth A], J [auth B], M [auth B], P [auth C]	1-(2-{3-[(1E)-N-(2-aminoethoxy)ethanimidoyl]phenyl}propan-2-yl)-3-(4-chloro-3-nitrophenyl)urea C20 H24 Cl N5 O4 MAIRRISEQUGPIE-DHRITJCHSA-N
IMP	E [auth A], I [auth B], N [auth C], Q [auth D]	INOSINIC ACID C10 H13 N4 O8 P GRSZFWQUAKGDAV-KQYNXXCUSA-N
PEG	H [auth A], L [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	G [auth A], K [auth B], O [auth C], R [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS	A, B, C, D	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.229 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.187 (Depositor) 
• R-Value Observed: 0.189 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34rv8

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.188	α = 90
b = 91.832	β = 103.75
c = 92.021	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: 2014-12-31 
Deposition Author(s): Kim, Y., Makowska-Grzyska, M., Gu, M., Kavitha, M., Hedstrom, L., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2014-12-31
  Type: Initial release
  
• Version 1.1: 2015-12-16
  Changes: Database references
• Version 1.2: 2017-02-08
  Changes: Structure summary
• Version 1.3: 2017-07-26
  Changes: Refinement description, Source and taxonomy
• Version 1.4: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2023-12-06
  Changes: Data collection