4MZ8

Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase, with an Internal Deletion of CBS Domain from Campylobacter jejuni complexed with inhibitor compound C91

PDB DOI: https://doi.org/10.2210/pdb4MZ8/pdb

Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
Organism(s): Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2013-09-29 Released: 2014-07-16
Deposition Author(s): Kim, Y., Makowska-Grzyska, M., Gu, M., Gorla, S.K., Hedstrom, L., Anderson, W.F., Joachimiak, A., CSGID, Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.217
R-Value Work: 0.176
R-Value Observed: 0.178

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase, with a Internal Deletion of CBS Domain from Campylobacter jejuni complexed with inhibitor compound C91

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

To be published.

Macromolecule Content

Total Structure Weight: 178.57 kDa
Atom Count: 11,176
Modelled Residue Count: 1,406
Deposited Residue Count: 1,624
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inosine-5'-monophosphate dehydrogenase	A, B, C, D	406	Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819	Mutation(s): 0 Gene Names: guaB, Cj1058c EC: 1.1.1.205
UniProt
Find proteins for Q0P9J4 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)) Explore Q0P9J4 Go to UniProtKB: Q0P9J4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q0P9J4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C91 Query on C91 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain GA [auth D] SDF format, chain O [auth B] SDF format, chain Z [auth C] MOL2 format, chain F [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain Z [auth C]	F [auth A], GA [auth D], O [auth B], Z [auth C]	N-(naphthalen-2-yl)-2-[2-(pyridin-2-yl)-1H-benzimidazol-1-yl]acetamide C₂₄ H₁₈ N₄ O XYCMWFINXXFAFG-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain GA [auth D] Focus chain O [auth B] Focus chain Z [auth C] Interactions & Density Focus chain F [auth A] Focus chain GA [auth D] Focus chain O [auth B] Focus chain Z [auth C]
IMP Query on IMP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain FA [auth D] SDF format, chain N [auth B] SDF format, chain Y [auth C] MOL2 format, chain E [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain N [auth B] MOL2 format, chain Y [auth C]	E [auth A], FA [auth D], N [auth B], Y [auth C]	INOSINIC ACID C₁₀ H₁₃ N₄ O₈ P GRSZFWQUAKGDAV-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain FA [auth D] Focus chain N [auth B] Focus chain Y [auth C] Interactions & Density Focus chain E [auth A] Focus chain FA [auth D] Focus chain N [auth B] Focus chain Y [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain EA [auth C] SDF format, chain G [auth A] SDF format, chain HA [auth D] SDF format, chain P [auth B] SDF format, chain R [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain R [auth B]	AA [auth C] EA [auth C] G [auth A] HA [auth D] P [auth B] AA [auth C], EA [auth C], G [auth A], HA [auth D], P [auth B], R [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth C] Focus chain EA [auth C] Focus chain G [auth A] Focus chain HA [auth D] Focus chain P [auth B] Focus chain R [auth B] Interactions & Density Focus chain AA [auth C] Focus chain EA [auth C] Focus chain G [auth A] Focus chain HA [auth D] Focus chain P [auth B] Focus chain R [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain IA [auth D] SDF format, chain T [auth B] SDF format, chain X [auth B] MOL2 format, chain H [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain X [auth B]	H [auth A], IA [auth D], T [auth B], X [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain IA [auth D] Focus chain T [auth B] Focus chain X [auth B] Interactions & Density Focus chain H [auth A] Focus chain IA [auth D] Focus chain T [auth B] Focus chain X [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain U [auth B] SDF format, chain V [auth B] MOL2 format, chain K [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B]	K [auth A], U [auth B], V [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain K [auth A] Focus chain U [auth B] Focus chain V [auth B]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain S [auth B] MOL2 format, chain J [auth A] MOL2 format, chain S [auth B]	J [auth A], S [auth B]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain S [auth B] Interactions & Density Focus chain J [auth A] Focus chain S [auth B]
2F2 Query on 2F2 Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A]	M [auth A]	dimethyl ether C₂ H₆ O LCGLNKUTAGEVQW-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain W [auth B] MOL2 format, chain I [auth A] MOL2 format, chain W [auth B]	I [auth A], W [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain W [auth B] Interactions & Density Focus chain I [auth A] Focus chain W [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain L [auth A] SDF format, chain Q [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain Q [auth B]	BA [auth C], CA [auth C], DA [auth C], L [auth A], Q [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain L [auth A] Focus chain Q [auth B] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain L [auth A] Focus chain Q [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.217
R-Value Work: 0.176
R-Value Observed: 0.178
Space Group: P 3₁ 2 1
Diffraction Data: https://doi.org/10.18430/m34mz8

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.46	α = 90
b = 114.46	β = 90
c = 256.314	γ = 120

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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-07-16

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2014-07-16
Type: Initial release
Version 1.1: 2017-05-17
Changes: Structure summary
Version 1.2: 2018-01-24
Changes: Structure summary
Version 1.3: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description