5UZS | pdb_00005uzs

Crystal Structure of Inosine 5'-monophosphate Dehydrogenase from Clostridium perfringens Complexed with IMP and P200

PDB DOI: https://doi.org/10.2210/pdb5UZS/pdb

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

Deposited: 2017-02-27 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)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free:
0.238 (Depositor), 0.238 (DCC)
R-Value Work:
0.170 (Depositor), 0.171 (DCC)
R-Value Observed:
0.173 (Depositor)

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 Inosine 5'-monophosphate Dehydrogenase from Clostridium perfringens Complexed with IMP and P200

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: 158.52 kDa
Atom Count: 10,821
Modelled Residue Count: 1,386
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	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 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IMP Query on IMP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain Q [auth C] SDF format, chain X [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain X [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain X [auth D]	E [auth A], J [auth B], Q [auth C], X [auth D]	INOSINIC ACID C₁₀ H₁₃ N₄ O₈ P GRSZFWQUAKGDAV-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain Q [auth C] Focus chain X [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain Q [auth C] Focus chain X [auth D]
8L4 Query on 8L4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain Y [auth D] SDF format, chain K [auth B] SDF format, chain R [auth C] MOL2 format, chain F [auth A] MOL2 format, chain Y [auth D] MOL2 format, chain K [auth B] MOL2 format, chain R [auth C] mmCIF format, chain F [auth A] mmCIF format, chain Y [auth D] mmCIF format, chain K [auth B] mmCIF format, chain R [auth C]	F [auth A], K [auth B], R [auth C], Y [auth D]	3-(2-{[(4-chlorophenyl)carbamoyl]amino}propan-2-yl)-N-hydroxybenzene-1-carboximidamide C₁₇ H₁₉ Cl N₄ O₂ NZOIAPIDYRJDOM-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain R [auth C] Focus chain Y [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain R [auth C] Focus chain Y [auth D]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain CA [auth D] MOL2 format, chain CA [auth D] mmCIF format, chain CA [auth D]	CA [auth D]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Interactions & Density Focus chain CA [auth D]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth B] SDF format, chain T [auth C] SDF format, chain H [auth A] SDF format, chain V [auth C] MOL2 format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain T [auth C] MOL2 format, chain H [auth A] MOL2 format, chain V [auth C] mmCIF format, chain G [auth A] mmCIF format, chain N [auth B] mmCIF format, chain T [auth C] mmCIF format, chain H [auth A] mmCIF format, chain V [auth C]	G [auth A], H [auth A], N [auth B], T [auth C], V [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain V [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain V [auth C]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain Z [auth D] SDF format, chain S [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain Z [auth D] MOL2 format, chain S [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain Z [auth D] mmCIF format, chain S [auth C]	AA [auth D] BA [auth D] I [auth A] L [auth B] S [auth C] AA [auth D], BA [auth D], I [auth A], L [auth B], S [auth C], Z [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain I [auth A] Focus chain L [auth B] Focus chain S [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain I [auth A] Focus chain L [auth B] Focus chain S [auth C] Focus chain Z [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain U [auth C] MOL2 format, chain M [auth B] MOL2 format, chain U [auth C] mmCIF format, chain M [auth B] mmCIF format, chain U [auth C]	M [auth B], U [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain U [auth C] Interactions & Density Focus chain M [auth B] Focus chain U [auth C]
K Query on K Download Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain W [auth C] MOL2 format, chain P [auth B] MOL2 format, chain W [auth C] mmCIF format, chain P [auth B] mmCIF format, chain W [auth C]	P [auth B], W [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain P [auth B] Focus chain W [auth C] Interactions & Density Focus chain P [auth B] Focus chain W [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY Query on ALY	A, B, C, D	L-PEPTIDE LINKING	C₈ H₁₆ N₂ O₃		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free: 0.238 (Depositor), 0.238 (DCC)
R-Value Work: 0.170 (Depositor), 0.171 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.124	α = 90
b = 144.396	β = 90
c = 87.527	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: 2017-03-22

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2017-03-22
Type: Initial release
Version 1.1: 2017-09-20
Changes: Author supporting evidence
Version 1.2: 2020-01-01
Changes: Author supporting evidence
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary