4MZ8 | pdb_00004mz8

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 (Depositor), 0.220 (DCC)
R-Value Work:
0.176 (Depositor), 0.180 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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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
Modeled Residue Count: 1,406
Deposited Residue Count: 1,624
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, 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] mmCIF format, chain F [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain O [auth B] mmCIF 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] mmCIF format, chain E [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain N [auth B] mmCIF 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] mmCIF format, chain AA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain P [auth B] mmCIF 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] mmCIF format, chain H [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain T [auth B] mmCIF 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] mmCIF format, chain K [auth A] mmCIF format, chain U [auth B] mmCIF 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] mmCIF format, chain J [auth A] mmCIF 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] mmCIF 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] mmCIF format, chain I [auth A] mmCIF 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] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain L [auth A] mmCIF 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 (Depositor), 0.220 (DCC)
R-Value Work: 0.176 (Depositor), 0.180 (DCC)
R-Value Observed: 0.178 (Depositor)

Diffraction Data: https://doi.org/10.18430/m34mz8

Space Group: P 3₁ 2 1

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