4MZ1 | pdb_00004mz1

Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase, with a Internal Deletion of CBS Domain from Campylobacter jejuni complexed with inhibitor compound P12

PDB DOI: https://doi.org/10.2210/pdb4MZ1/pdb

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

Deposited: 2013-09-28 Released: 2014-01-01
Deposition Author(s): Kim, Y., Makowska-Grzyska, M., Gu, M., Anderson, W.F., Joachimiak, A., CSGID, Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.212 (Depositor), 0.210 (DCC)
R-Value Work:
0.172 (Depositor), 0.170 (DCC)
R-Value Observed:
0.174 (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 P12

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

To be published.

Macromolecule Content

Total Structure Weight: 126.52 kDa
Atom Count: 8,427
Modeled Residue Count: 1,069
Deposited Residue Count: 1,155
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	385	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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2F1 Query on 2F1 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain T [auth C] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain T [auth C] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain T [auth C]	E [auth A], L [auth B], T [auth C]	1-(4-bromophenyl)-3-{2-[3-(prop-1-en-2-yl)phenyl]propan-2-yl}urea C₁₉ H₂₁ Br N₂ O UILINQCNOUGMOK-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain T [auth C] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain T [auth C]
IMP Query on IMP Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain K [auth B] SDF format, chain S [auth C] MOL2 format, chain D [auth A] MOL2 format, chain K [auth B] MOL2 format, chain S [auth C] mmCIF format, chain D [auth A] mmCIF format, chain K [auth B] mmCIF format, chain S [auth C]	D [auth A], K [auth B], S [auth C]	INOSINIC ACID C₁₀ H₁₃ N₄ O₈ P GRSZFWQUAKGDAV-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Focus chain S [auth C] Interactions & Density Focus chain D [auth A] Focus chain K [auth B] Focus chain S [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain V [auth C] MOL2 format, chain G [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain V [auth C] mmCIF format, chain G [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain V [auth C]	G [auth A], O [auth B], P [auth B], V [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain V [auth C] Interactions & Density Focus chain G [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain V [auth C]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain Q [auth B] SDF format, chain W [auth C] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain W [auth C] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain W [auth C]	H [auth A] I [auth A] J [auth A] N [auth B] Q [auth B] H [auth A], I [auth A], J [auth A], N [auth B], Q [auth B], W [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain Q [auth B] Focus chain W [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain Q [auth B] Focus chain W [auth C]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain X [auth C] MOL2 format, chain R [auth C] MOL2 format, chain X [auth C] mmCIF format, chain R [auth C] mmCIF format, chain X [auth C]	R [auth C], X [auth C]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain R [auth C] Focus chain X [auth C] Interactions & Density Focus chain R [auth C] Focus chain X [auth C]
K Query on K Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth B] SDF format, chain U [auth C] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain U [auth C] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B] mmCIF format, chain U [auth C]	F [auth A], M [auth B], U [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain M [auth B] Focus chain U [auth C] Interactions & Density Focus chain F [auth A] Focus chain M [auth B] Focus chain U [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.212 (Depositor), 0.210 (DCC)
R-Value Work: 0.172 (Depositor), 0.170 (DCC)
R-Value Observed: 0.174 (Depositor)

Diffraction Data: https://doi.org/10.18430/m34mz1

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.062	α = 90
b = 118.062	β = 90
c = 435.16	γ = 90

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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-01-01

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2014-01-01
Type: Initial release
Version 1.1: 2017-08-02
Changes: Refinement description, Source and taxonomy
Version 1.2: 2018-01-24
Changes: Structure summary
Version 1.3: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description