5UXE | pdb_00005uxe

Crystal Structure of Inosine 5'-monophosphate Dehydrogenase from Clostridium perfringens Complexed with IMP and P178

PDB DOI: https://doi.org/10.2210/pdb5UXE/pdb

Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
Organism(s): Clostridium perfringens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-02-22 Released: 2017-03-08
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: 2.10 Å
R-Value Free:
0.223 (Depositor), 0.220 (DCC)
R-Value Work:
0.173 (Depositor), 0.170 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
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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 P178

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: 157.56 kDa
Atom Count: 10,766
Modelled Residue Count: 1,374
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	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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8LA Query on 8LA Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain N [auth C] SDF format, chain R [auth D] SDF format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain N [auth C] MOL2 format, chain R [auth D] MOL2 format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain N [auth C] mmCIF format, chain R [auth D] mmCIF format, chain F [auth A]	F [auth A], I [auth B], N [auth C], R [auth D]	N-[4-chloro-3-(alpha-D-ribofuranosyloxy)phenyl]-N'-{2-[3-(prop-1-en-2-yl)phenyl]propan-2-yl}urea C₂₄ H₂₉ Cl N₂ O₆ DGCHEIBDGDMRPM-YSFYHYPLSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain R [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 M [auth C] SDF format, chain Q [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth D]	E [auth A], H [auth B], M [auth C], Q [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 M [auth C] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain M [auth C] Focus chain Q [auth D]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain S [auth D] MOL2 format, chain J [auth B] MOL2 format, chain S [auth D] mmCIF format, chain J [auth B] mmCIF format, chain S [auth D]	J [auth B], S [auth D]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain J [auth B] Focus chain S [auth D] Interactions & Density Focus chain J [auth B] Focus chain S [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain O [auth C] MOL2 format, chain O [auth C] mmCIF format, chain O [auth C]	O [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain O [auth C] Interactions & Density Focus chain O [auth C]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain L [auth C] MOL2 format, chain L [auth C] mmCIF format, chain L [auth C]	L [auth C]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain L [auth C] Interactions & Density Focus chain L [auth C]
K Query on K Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain P [auth D] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain P [auth D] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain P [auth D]	G [auth A], K [auth B], P [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.223 (Depositor), 0.220 (DCC)
R-Value Work: 0.173 (Depositor), 0.170 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.937	α = 90
b = 119.101	β = 102.86
c = 96.971	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

Deposition Data

Released Date: 2017-03-08

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2017-03-08
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description