6YJF | pdb_00006yjf

Plasmoodium vivax phosphoglycerate kinase bound to nitrofuran inhibitor from PEGSmear at pH 6.5

PDB DOI: https://doi.org/10.2210/pdb6YJF/pdb

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

Deposited: 2020-04-03 Released: 2021-04-14
Deposition Author(s): Hyvonen, M., Brear, P., Blaszczyk, B.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.225 (Depositor), 0.223 (DCC)
R-Value Work:
0.191 (Depositor)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Phosphoglycerate Kinase as a potential target for antimalarial therapy

King, L., Brear, P., Bourgard, C., Cassiano, C., Mota, D., Blaszczyk, B.K., Tomaz, K., Khedim, M., Furlan, M., Ramos, P., Andresen, E., Tarczykowska, A., Tiburcio, L., Kurowska, A., Sulskis, D., Oliver, S., Grotli, M., Massirer, K., Saphire, E., Burmann, B., Witkowski, B., Costa, F., Sunnerhagen, P., Hyvonen, M., Bilsland, E.

To be published.

Macromolecule Content

Total Structure Weight: 45.61 kDa
Atom Count: 3,485
Modeled Residue Count: 416
Deposited Residue Count: 416
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoglycerate kinase	A	416	Plasmodium vivax	Mutation(s): 0 Gene Names: PVC01_070025900, PVP01_0721000, PVT01_070026100 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
OTQ (Subject of Investigation/LOI) Query on OTQ 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]	(2~{S})-2-(5-nitrofuran-2-yl)-2,3,5,6,7,8-hexahydro-1~{H}-[1]benzothiolo[2,3-d]pyrimidin-4-one C₁₄ H₁₃ N₃ O₄ S MOKSPNCNIWVHBB-LBPRGKRZSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-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: 1.85 Å
R-Value Free: 0.225 (Depositor), 0.223 (DCC)
R-Value Work: 0.191 (Depositor)
R-Value Observed: 0.193 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.594	α = 90
b = 82.315	β = 90
c = 124.495	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
BUSTER	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-04-14

Deposition Author(s):

Blaszczyk, B.K.

Revision History (Full details and data files)

Version 1.0: 2021-04-14
Type: Initial release
Version 2.0: 2022-05-11
Changes: Database references, Non-polymer description, Structure summary
Version 2.1: 2024-01-24
Changes: Data collection, 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.