5VT4 | pdb_00005vt4

Sco GlgEI-V279S in complex with a pyrolidene-based methyl-phosphonate compound

PDB DOI: https://doi.org/10.2210/pdb5VT4/pdb

Classification: TRANSFERASE
Organism(s): Streptomyces coelicolor A3(2)
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2017-05-15 Released: 2017-06-07
Deposition Author(s): Petit, C., Ronning, D.R., Lindenberger, J.J.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.21 Å
R-Value Free:
0.239 (Depositor), 0.243 (DCC)
R-Value Work:
0.207 (Depositor), 0.215 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Zwitterionic pyrrolidene-phosphonates: inhibitors of the glycoside hydrolase-like phosphorylase Streptomyces coelicolor GlgEI-V279S.

Veleti, S.K., Petit, C., Ronning, D.R., Sucheck, S.J.

(2017) Org Biomol Chem 15: 3884-3891

PubMed: 28422240 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1039/c7ob00388a
Primary Citation Related Structures:
5VSJ, 5VT4

PubMed Abstract:
We synthesized and evaluated new zwitterionic inhibitors against glycoside hydrolase-like phosphorylase Streptomyces coelicolor (Sco) GlgEI-V279S which plays a role in α-glucan biosynthesis. Sco GlgEI-V279S serves as a model enzyme for validated anti-tuberculosis (TB) target Mycobacterium tuberculosis (Mtb) GlgE. Pyrrolidine inhibitors 5 and 6 were designed based on transition state considerations and incorporate a phosphonate on the pyrrolidine moiety to expand the interaction network between the inhibitor and the enzyme active site. Compounds 5 and 6 inhibited Sco GlgEI-V279S with K _i = 45 ± 4 μM and 95 ± 16 μM, respectively, and crystal structures of Sco GlgE-V279S-5 and Sco GlgE-V279S-6 were obtained at a 3.2 Å and 2.5 Å resolution, respectively.

Organizational Affiliation

Department of Chemistry and Biochemistry and School of Green Chemistry and Engineering, The University of Toledo, 2801 W. Bancroft Street, Toledo, Ohio 43606, USA. steve.sucheck@utoledo.edu donald.ronning@utoledo.edu.

Macromolecule Content

Total Structure Weight: 298.39 kDa
Atom Count: 20,458
Modeled Residue Count: 2,580
Deposited Residue Count: 2,652
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1	A, B, C, D	663	Streptomyces coelicolor A3(2)	Mutation(s): 1 Gene Names: glgE1, pep1, pep1A, pep1I, SCO5443, SC6A11.19c EC: 2.4.99.16
UniProt
Find proteins for Q9L1K2 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)) Explore Q9L1K2 Go to UniProtKB: Q9L1K2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9L1K2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9KJ Query on 9KJ Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C], H [auth D]	{[(2R,3R,4R,5R)-3-(alpha-D-glucopyranosyloxy)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-1-yl]methyl}phosphonic acid C₁₃ H₂₆ N O₁₂ P QVTCDBMCRXGRKE-DFIZWEOJSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.21 Å
R-Value Free: 0.239 (Depositor), 0.243 (DCC)
R-Value Work: 0.207 (Depositor), 0.215 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.851	α = 90
b = 113.851	β = 90
c = 312.49	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	model building
HKL-2000	data scaling
HKL-2000	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-06-07

Deposition Author(s):

Petit, C.

Ronning, D.R.

Lindenberger, J.J.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI105084

Revision History (Full details and data files)

Version 1.0: 2017-06-07
Type: Initial release
Version 1.1: 2017-10-04
Changes: Author supporting evidence, Refinement description
Version 1.2: 2019-12-11
Changes: Author supporting evidence
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations
Version 2.1: 2023-10-04
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary