8PRY

Crystal structure of Trypanosoma cruzi glycerol kinase

PDB DOI: https://doi.org/10.2210/pdb8PRY/pdb

Classification: TRANSFERASE
Organism(s): Trypanosoma cruzi
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-07-12 Released: 2024-07-24
Deposition Author(s): Lipinski, O., Sonani, R.R., Dubin, G.
Funding Organization(s): Polish National Science Centre

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free: 0.238
R-Value Work: 0.176
R-Value Observed: 0.179

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of Trypanosoma cruzi glycerol kinase in complex with glycerol

Lipinski, O., Sonani, R.R., Dubin, G.

To be published.

Macromolecule Content

Total Structure Weight: 233.45 kDa
Atom Count: 16,378
Modelled Residue Count: 2,046
Deposited Residue Count: 2,092
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
glycerol kinase	A, B, C, D	523	Trypanosoma cruzi	Mutation(s): 0 Gene Names: C4B63_2g784
UniProt
Find proteins for A0A2V2W444 (Trypanosoma cruzi) Explore A0A2V2W444 Go to UniProtKB: A0A2V2W444
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2V2W444
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD Query on CSD	A, B, C, D	L-PEPTIDE LINKING	C₃ H₇ N O₄ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free: 0.238
R-Value Work: 0.176
R-Value Observed: 0.179
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.779	α = 117.35
b = 89.321	β = 88.99
c = 97.155	γ = 93.68

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-07-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Polish National Science Centre	Poland	2020/39/B/NZ1/01551

Revision History (Full details and data files)

Version 1.0: 2024-07-24
Type: Initial release

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 R01GM133198.