5UZE | pdb_00005uze

Crystal Structure of Inosine 5'-monophosphate Dehydrogenase from Clostridium perfringens Complexed with IMP and P182

PDB DOI: https://doi.org/10.2210/pdb5UZE/pdb

Classification: oxidoreductase/oxidoreductase inhibitor
Organism(s): Clostridium perfringens ATCC 13124
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-02-26 Released: 2017-03-22
Deposition Author(s): Maltseva, N., Kim, Y., Mulligan, R., Makowska-Grzyska, M., Gu, M., Gollapalli, D.R., Hedstrom, L., Joachimiak, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free:
0.255 (Depositor), 0.260 (DCC)
R-Value Work:
0.194 (Depositor), 0.190 (DCC)
R-Value Observed:
0.197 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of Inosine 5'-monophosphate Dehydrogenase from Clostridium perfringens Complexed with IMP and P182

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

To be published.

Macromolecule Content

Total Structure Weight: 157.32 kDa
Atom Count: 10,463
Modelled Residue Count: 1,367
Deposited Residue Count: 1,452
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,Inosine-5'-monophosphate dehydrogenase	A, B, C, D	363	Clostridium perfringens ATCC 13124	Mutation(s): 0 Gene Names: guaB, CPF_2558 EC: 1.1.1.205
UniProt
Find proteins for A0A0H2YRZ7 (Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A)) Explore A0A0H2YRZ7 Go to UniProtKB: A0A0H2YRZ7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H2YRZ7
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8L1 Query on 8L1 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain M [auth C] SDF format, chain O [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D]	F [auth A], I [auth B], M [auth C], O [auth D]	N-{4-chloro-3-[4-(trifluoromethyl)-1,3-thiazol-2-yl]phenyl}-N'-(2-{3-[(1E)-N-hydroxyethanimidoyl]phenyl}propan-2-yl)urea C₂₂ H₂₀ Cl F₃ N₄ O₂ S RTMPYAODZXTXJR-PNQUVVCRSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain O [auth D]
IMP Query on IMP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D]	E [auth A], H [auth B], L [auth C], N [auth D]	INOSINIC ACID C₁₀ H₁₃ N₄ O₈ P GRSZFWQUAKGDAV-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain N [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B]	G [auth A], J [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free: 0.255 (Depositor), 0.260 (DCC)
R-Value Work: 0.194 (Depositor), 0.190 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.777	α = 110.03
b = 77.662	β = 103.99
c = 80.321	γ = 105.46

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-03-22

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2017-03-22
Type: Initial release
Version 1.1: 2024-03-06
Changes: Advisory, Data collection, Database references, Derived calculations