5UPY | pdb_00005upy

Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Listeria Monocytogenes in the complex with IMP and Q21

• PDB DOI: https://doi.org/10.2210/pdb5UPY/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Listeria monocytogenes EGD-e
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-02-04 Released: 2017-04-05 
• Deposition Author(s): Kim, Y., Makowska-Grzyska, M., Osipiuk, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.208 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Listeria Monocytogenes in the complex with IMP and Q21

Kim, Y., Makowska-Grzyska, M., Osipiuk, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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: 39.71 kDa 
• Atom Count: 2,780 
• Modeled Residue Count: 350 
• Deposited Residue Count: 364 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inosine-5'-monophosphate dehydrogenase	A	364	Listeria monocytogenes EGD-e	Mutation(s): 0  Gene Names: guaB EC: 1.1.1.205
UniProt
Find proteins for Q926Y9 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q926Y9  Go to UniProtKB:  Q926Y9

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Q21	C [auth A]	(2S)-2-(naphthalen-1-yloxy)-N-[2-(pyridin-4-yl)-1,3-benzoxazol-5-yl]propanamide C25 H19 N3 O3 QCNXGTHMVPSAAC-INIZCTEOSA-N
IMP	B [auth A]	INOSINIC ACID C10 H13 N4 O8 P GRSZFWQUAKGDAV-KQYNXXCUSA-N
GOL	E [auth A], F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	H [auth A], I [auth A], J [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.208 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: I 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.165	α = 90
b = 174.165	β = 90
c = 174.165	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-04-05 
Deposition Author(s): Kim, Y., Makowska-Grzyska, M., Osipiuk, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2017-04-05
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description