7S2P

Crystal structure of the F337L mutation of Trypanosoma cruzi glucokinase in complex with inhibitor CBZ-GlcN

PDB DOI: https://doi.org/10.2210/pdb7S2P/pdb

Classification: TRANSFERASE
Organism(s): Trypanosoma cruzi strain CL Brener
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2021-09-03 Released: 2021-10-06
Deposition Author(s): Carey, S.M., Nettles, R.B., Daneshian, L., Chruszcz, M., D'Antonio, E.L.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.255
R-Value Work: 0.202
R-Value Observed: 0.204

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of the F337L mutation of Trypanosoma cruzi glucokinase in complex with inhibitor CBZ-GlcN

Carey, S.M., Nettles, R.B., Daneshian, L., Chruszcz, M., D'Antonio, E.L.

To be published.

Macromolecule Content

Total Structure Weight: 85.11 kDa
Atom Count: 5,728
Modelled Residue Count: 734
Deposited Residue Count: 762
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucokinase 1	A, B	381	Trypanosoma cruzi strain CL Brener	Mutation(s): 1 Gene Names: Tc00.1047053510187.100 EC: 2.7.1.2
UniProt
Find proteins for Q4E4E1 (Trypanosoma cruzi (strain CL Brener)) Explore Q4E4E1 Go to UniProtKB: Q4E4E1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q4E4E1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4UZ (Subject of Investigation/LOI) Query on 4UZ Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	2-{[(benzyloxy)carbonyl]amino}-2-deoxy-beta-D-glucopyranose C₁₄ H₁₉ N O₇ FRTOTMQAWIIMKK-SYLRKERUSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.255
R-Value Work: 0.202
R-Value Observed: 0.204
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.227	α = 90
b = 78.951	β = 94.86
c = 77.027	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-10-06

Deposition Author(s):

D'Antonio, E.L.

Funding Organization	Location	Grant Number
Other government	United States	University of South Carolina, Office of the Vice President for Research, Magellan Program

Revision History (Full details and data files)

Version 1.0: 2021-10-06
Type: Initial release
Version 1.1: 2021-10-20
Changes: Experimental preparation
Version 1.2: 2023-10-18
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.