6MGR

Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Campylobacter jejuni in the complex with inhibitor Oxanosine monophosphate

PDB DOI: https://doi.org/10.2210/pdb6MGR/pdb

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

Deposited: 2018-09-14 Released: 2018-10-24
Deposition Author(s): Kim, Y., Maltseva, N., Yu, R., Hedstrom, L., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free: 0.202
R-Value Work: 0.173
R-Value Observed: 0.175

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 the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Campylobacter jejuni in the complex with inhibitor Oxanosine Monophosphate

Kim, Y., Maltseva, N., Yu, R., Hedstrom, L., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 168.22 kDa
Atom Count: 11,602
Modelled Residue Count: 1,449
Deposited Residue Count: 1,540
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 monophosphate dehydrogenase	A, B, C, D	385	Campylobacter jejuni	Mutation(s): 0 Gene Names: C9J79_08320 EC: 1.1.1.205
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JQS Query on JQS Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain IA [auth D] SDF format, chain O [auth B] SDF format, chain Z [auth C] MOL2 format, chain E [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain E [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain O [auth B] mmCIF format, chain Z [auth C]	E [auth A], IA [auth D], O [auth B], Z [auth C]	5-[(Z)-(aminomethylidene)amino]-1-(5-O-phosphono-beta-D-ribofuranosyl)-1H-imidazole-4-carboxylic acid C₁₀ H₁₅ N₄ O₉ P CEVAZLJDKSQTJT-FJGDRVTGSA-N		Interactions Focus chain E [auth A] Focus chain IA [auth D] Focus chain O [auth B] Focus chain Z [auth C] Interactions & Density Focus chain E [auth A] Focus chain IA [auth D] Focus chain O [auth B] Focus chain Z [auth C]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain L [auth A] SDF format, chain X [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain X [auth B] mmCIF format, chain GA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain X [auth B]	GA [auth C], L [auth A], X [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain GA [auth C] Focus chain L [auth A] Focus chain X [auth B] Interactions & Density Focus chain GA [auth C] Focus chain L [auth A] Focus chain X [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain F [auth A] SDF format, chain FA [auth C] SDF format, chain G [auth A] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain LA [auth D] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain QA [auth D] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain V [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain V [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain LA [auth D] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth D] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain V [auth B]	AA [auth C] CA [auth C] DA [auth C] EA [auth C] F [auth A] AA [auth C], CA [auth C], DA [auth C], EA [auth C], F [auth A], FA [auth C], G [auth A], JA [auth D], KA [auth D], LA [auth D], P [auth B], Q [auth B], QA [auth D], R [auth B], S [auth B], T [auth B], V [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain P [auth B] Focus chain Q [auth B] Focus chain QA [auth D] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain V [auth B] Interactions & Density Focus chain AA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain P [auth B] Focus chain Q [auth B] Focus chain QA [auth D] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain V [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain HA [auth D] SDF format, chain M [auth A] SDF format, chain N [auth B] SDF format, chain U [auth B] SDF format, chain Y [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain N [auth B] MOL2 format, chain U [auth B] MOL2 format, chain Y [auth C] mmCIF format, chain HA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain N [auth B] mmCIF format, chain U [auth B] mmCIF format, chain Y [auth C]	HA [auth D], M [auth A], N [auth B], U [auth B], Y [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain HA [auth D] Focus chain M [auth A] Focus chain N [auth B] Focus chain U [auth B] Focus chain Y [auth C] Interactions & Density Focus chain HA [auth D] Focus chain M [auth A] Focus chain N [auth B] Focus chain U [auth B] Focus chain Y [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain OA [auth D] SDF format, chain PA [auth D] SDF format, chain W [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain W [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain OA [auth D] mmCIF format, chain PA [auth D] mmCIF format, chain W [auth B]	BA [auth C] H [auth A] I [auth A] J [auth A] K [auth A] BA [auth C], H [auth A], I [auth A], J [auth A], K [auth A], MA [auth D], NA [auth D], OA [auth D], PA [auth D], W [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth C] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain W [auth B] Interactions & Density Focus chain BA [auth C] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain W [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free: 0.202
R-Value Work: 0.173
R-Value Observed: 0.175
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.343	α = 90
b = 119.592	β = 89.99
c = 119.307	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-10-24

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2018-10-24
Type: Initial release
Version 1.1: 2019-12-18
Changes: Author supporting evidence
Version 1.2: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description