6VYG | pdb_00006vyg

Cryo-EM structure of Plasmodium vivax hexokinase (Closed state)

PDB DOI: https://doi.org/10.2210/pdb6VYG/pdb
EM Map EMD-21459: EMDB EMDataResource

Classification: TRANSFERASE
Organism(s): Plasmodium vivax
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-02-26 Released: 2020-05-06
Deposition Author(s): Srivastava, S.S., Darling, J.E., Suryadi, J., Morris, J.C., Drew, M.E., Subramaniam, S.
Funding Organization(s): Canada Excellence Research Chair Award

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 6VYG

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

Literature

Plasmodium vivax and human hexokinases share similar active sites but display distinct quaternary architectures

Srivastava, S.S., Darling, J.E., Suryadi, J., Morris, J.C., Drew, M.E., Subramaniam, S.

(2020) IUCrJ 7: 453-461

DOI: https://doi.org/10.1107/S2052252520002456

Macromolecule Content

Total Structure Weight: 227.41 kDa
Atom Count: 13,616
Modeled Residue Count: 1,732
Deposited Residue Count: 2,020
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphotransferase	A, B, C, D	505	Plasmodium vivax	Mutation(s): 0 Gene Names: PVC01_110030900, PVP01_1125500, PVT01_110029900 EC: 2.7.1
UniProt
Find proteins for A5K274 (Plasmodium vivax (strain Salvador I)) Explore A5K274 Go to UniProtKB: A5K274
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A5K274
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	3.0

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-05-06

Deposition Author(s):

Srivastava, S.S.

Subramaniam, S.

Funding Organization	Location	Grant Number
Canada Excellence Research Chair Award	Canada	--

Revision History (Full details and data files)

Version 1.0: 2020-05-06
Type: Initial release
Version 1.1: 2024-11-20
Changes: Data collection, Database references, Structure summary
Version 1.2: 2025-06-04
Changes: Data collection

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.