6Y3A | pdb_00006y3a

Structure of Plasmodium vivax phosphoglycerate kinase

PDB DOI: https://doi.org/10.2210/pdb6Y3A/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Plasmodium vivax
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-02-17 Released: 2020-02-26
Deposition Author(s): Blaszczyk, B.K., Hyvonen, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free:
0.195 (Depositor), 0.196 (DCC)
R-Value Work:
0.163 (Depositor), 0.166 (DCC)
R-Value Observed:
0.165 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Phosphoglycerate Kinase as a potential target for antimalarial therapy

Bilsland, E., Costa, F., Blaszczyk, B.K., Hyvonen, M., Sunnerhagen, P.

To be published.

Macromolecule Content

Total Structure Weight: 46.37 kDa
Atom Count: 3,699
Modeled Residue Count: 416
Deposited Residue Count: 424
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoglycerate kinase	A	424	Plasmodium vivax	Mutation(s): 0 Gene Names: PVX_099535 EC: 2.7.2.3
UniProt
Find proteins for A5K6T9 (Plasmodium vivax (strain Salvador I)) Explore A5K6T9 Go to UniProtKB: A5K6T9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A5K6T9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BR Query on BR Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free: 0.195 (Depositor), 0.196 (DCC)
R-Value Work: 0.163 (Depositor), 0.166 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.34	α = 90
b = 84.12	β = 90
c = 125.52	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
xia2	data reduction
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-02-26

Deposition Author(s):

Blaszczyk, B.K.

Revision History (Full details and data files)

Version 1.0: 2020-02-26
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.