5UWX | pdb_00005uwx

Crystal Structure of Inosine 5'-monophosphate Dehydrogenase from Clostridium perfringens Complexed with IMP and P176

PDB DOI: https://doi.org/10.2210/pdb5UWX/pdb

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

Deposited: 2017-02-21 Released: 2017-03-01
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)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.197 (Depositor), 0.200 (DCC)
R-Value Work:
0.163 (Depositor), 0.160 (DCC)
R-Value Observed:
0.164 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Crystal Structure of Inosine 5'-monophosphate Dehydrogenase from Clostridium perfringens Complexed with IMP and P176

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: 157.83 kDa
Atom Count: 11,017
Modelled Residue Count: 1,377
Deposited Residue Count: 1,452
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,Inosine-5'-monophosphate dehydrogenase	A, B, C, D	363	Clostridium perfringens	Mutation(s): 0 Gene Names: guaB_2, guaB, ERS852446_02285, JFP838_13815 EC: 1.1.1.205
UniProt
Find proteins for A0A127ELD1 (Clostridium perfringens) Explore A0A127ELD1 Go to UniProtKB: A0A127ELD1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A127ELD1
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8L7 Query on 8L7 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain M [auth C] SDF format, chain Q [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth D]	E [auth A], I [auth B], M [auth C], Q [auth D]	N-{2-chloro-5-[({2-[3-(prop-1-en-2-yl)phenyl]propan-2-yl}carbamoyl)amino]phenyl}-alpha-D-ribofuranosylamine C₂₄ H₃₀ Cl N₃ O₅ RGENKIJBZZZCQP-YSFYHYPLSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D]
IMP Query on IMP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain R [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain R [auth D] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain R [auth D]	F [auth A], J [auth B], N [auth C], R [auth D]	INOSINIC ACID C₁₀ H₁₃ N₄ O₈ P GRSZFWQUAKGDAV-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D]
MRD Query on MRD Download Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain P [auth C] SDF format, chain S [auth D] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain P [auth C] mmCIF format, chain S [auth D]	G [auth A], K [auth B], P [auth C], S [auth D]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain S [auth D] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain S [auth D]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain O [auth C] SDF format, chain T [auth D] MOL2 format, chain H [auth A] MOL2 format, chain O [auth C] MOL2 format, chain T [auth D] mmCIF format, chain H [auth A] mmCIF format, chain O [auth C] mmCIF format, chain T [auth D]	H [auth A], O [auth C], T [auth D]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain O [auth C] Focus chain T [auth D] Interactions & Density Focus chain H [auth A] Focus chain O [auth C] Focus chain T [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.197 (Depositor), 0.200 (DCC)
R-Value Work: 0.163 (Depositor), 0.160 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.278	α = 90
b = 118.943	β = 102.88
c = 96.992	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-03-01

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: 2017-03-01
Type: Initial release
Version 1.1: 2017-08-09
Changes: Database references
Version 1.2: 2017-08-23
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.3: 2017-09-20
Changes: Author supporting evidence
Version 1.4: 2022-03-23
Changes: Author supporting evidence, Database references
Version 1.5: 2024-05-22
Changes: Data collection