5UQF

Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Campylobacter jejuni in the complex with IMP and the inhibitor P225

PDB DOI: https://doi.org/10.2210/pdb5UQF/pdb

Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
Organism(s): Campylobacter jejuni subsp. jejuni, Campylobacter jejuni subsp. jejuni CG8486
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-02-08 Released: 2017-03-01
Deposition Author(s): Kim, Y., Maltseva, N., Makowska-Grzyska, M., Gu, M., Gollapalli, D., Hedstrom, L., 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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.73 Å
R-Value Free: 0.228
R-Value Work: 0.175
R-Value Observed: 0.177

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Campylobacter jejuni in the complex with IMP and the inhibitor P225

Kim, Y., Maltseva, N., Makowska-Grzyska, M., Gu, M., Gollapalli, D., Hedstrom, L., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 134.53 kDa
Atom Count: 8,232
Modelled Residue Count: 1,064
Deposited Residue Count: 1,218
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inosine-5'-monophosphate dehydrogenase	A, B, C	406	Campylobacter jejuni subsp. jejuni, Campylobacter jejuni subsp. jejuni CG8486 This entity is chimeric	Mutation(s): 0 Gene Names: guaB, CJ14980A_1064, Cj8486_1016 EC: 1.1.1.205
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8KY Query on 8KY Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain O [auth B] SDF format, chain Z [auth C] MOL2 format, chain E [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain E [auth A] mmCIF format, chain O [auth B] mmCIF format, chain Z [auth C]	E [auth A], O [auth B], Z [auth C]	{2-chloro-5-[({2-[3-(prop-1-en-2-yl)phenyl]propan-2-yl}carbamoyl)amino]phenoxy}acetic acid C₂₁ H₂₃ Cl N₂ O₄ NIAYZIDQFFFUTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain O [auth B] Focus chain Z [auth C] Interactions & Density Focus chain E [auth A] Focus chain O [auth B] Focus chain Z [auth C]
IMP Query on IMP Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain Y [auth C] SDF format, chain D [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain D [auth A] mmCIF format, chain N [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain D [auth A]	D [auth A], N [auth B], Y [auth C]	INOSINIC ACID C₁₀ H₁₃ N₄ O₈ P GRSZFWQUAKGDAV-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Focus chain N [auth B] Focus chain Y [auth C] Interactions & Density Focus chain D [auth A] Focus chain N [auth B] Focus chain Y [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B]	BA [auth C] CA [auth C] G [auth A] H [auth A] I [auth A] BA [auth C], CA [auth C], G [auth A], H [auth A], I [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain V [auth B] MOL2 format, chain DA [auth C] MOL2 format, chain V [auth B] mmCIF format, chain DA [auth C] mmCIF format, chain V [auth B]	DA [auth C], V [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain V [auth B] Interactions & Density Focus chain DA [auth C] Focus chain V [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B]	J [auth A] K [auth A] L [auth A] M [auth A] W [auth B] J [auth A], K [auth A], L [auth A], M [auth A], W [auth B], X [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain W [auth B] Focus chain X [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain F [auth A] SDF format, chain P [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain P [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain P [auth B]	AA [auth C], F [auth A], P [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain F [auth A] Focus chain P [auth B] Interactions & Density Focus chain AA [auth C] Focus chain F [auth A] Focus chain P [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain FA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C]	EA [auth C], FA [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain EA [auth C] Focus chain FA [auth C] Interactions & Density Focus chain EA [auth C] Focus chain FA [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.73 Å
R-Value Free: 0.228
R-Value Work: 0.175
R-Value Observed: 0.177
Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.526	α = 90
b = 118.526	β = 90
c = 451.298	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-03-01

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

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

Revision History (Full details and data files)

Version 1.0: 2017-03-01
Type: Initial release
Version 1.1: 2017-03-08
Changes: Structure summary
Version 1.2: 2017-09-20
Changes: Author supporting evidence
Version 1.3: 2020-01-01
Changes: Author supporting evidence
Version 1.4: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description