9UIZ | pdb_00009uiz

PLASMODIUM VIVAX PHENYLALANYL-TRNA SYNTHETASE IN COMPLEX WITH PHE-AMS IN SPACE GROUP P21

PDB DOI: https://doi.org/10.2210/pdb9UIZ/pdb

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

Deposited: 2025-04-16 Released: 2026-11-04
Deposition Author(s): Mutharasappan, N., Manickam, Y., Bagale, S., Pradeepkumar, P.I., Sharma, A.
Funding Organization(s): Department of Science & Technology (DST, India), Department of Biotechnology (DBT, India), Indian Council of Medical Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.266 (Depositor), 0.267 (DCC)
R-Value Work:
0.235 (Depositor), 0.235 (DCC)
R-Value Observed:
0.236 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

PLASMODIUM VIVAX PHENYLALANYL-TRNA SYNTHETASE IN COMPLEX WITH L-PHE

Mutharasappan, N., Manickam, Y., Sharma, A.

To be published.

Macromolecule Content

Total Structure Weight: 214.94 kDa
Atom Count: 12,760
Modeled Residue Count: 1,650
Deposited Residue Count: 1,834
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phenylalanyl-tRNA synthetase beta chain, putative	A, C	299	Plasmodium vivax	Mutation(s): 0 Gene Names: PVX_081300 EC: 6.1.1.20
UniProt
Find proteins for A5K9S0 (Plasmodium vivax (strain Salvador I)) Explore A5K9S0 Go to UniProtKB: A5K9S0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A5K9S0
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phenylalanyl-tRNA synthetase beta chain, putative	B, D	618	Plasmodium vivax	Mutation(s): 0 Gene Names: PVX_090880 EC: 6.1.1.20
UniProt
Find proteins for A5K464 (Plasmodium vivax (strain Salvador I)) Explore A5K464 Go to UniProtKB: A5K464
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A5K464
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
W5Y (Subject of Investigation/LOI) Query on W5Y Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth C] MOL2 format, chain E [auth A] MOL2 format, chain H [auth C] mmCIF format, chain E [auth A] mmCIF format, chain H [auth C]	E [auth A], H [auth C]	5'-O-(L-phenylalanylsulfamoyl)adenosine C₁₉ H₂₃ N₇ O₇ S QGOJGCAOMCBQFJ-QTOWJTHWSA-N		Interactions Focus chain E [auth A] Focus chain H [auth C] Interactions & Density Focus chain E [auth A] Focus chain H [auth C]
PO4 (Subject of Investigation/LOI) Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth C] MOL2 format, chain F [auth A] MOL2 format, chain I [auth C] mmCIF format, chain F [auth A] mmCIF format, chain I [auth C]	F [auth A], I [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain I [auth C] Interactions & Density Focus chain F [auth A] Focus chain I [auth C]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain J [auth C] MOL2 format, chain G [auth B] MOL2 format, chain J [auth C] mmCIF format, chain G [auth B] mmCIF format, chain J [auth C]	G [auth B], J [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain J [auth C] Interactions & Density Focus chain G [auth B] Focus chain J [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.266 (Depositor), 0.267 (DCC)
R-Value Work: 0.235 (Depositor), 0.235 (DCC)
R-Value Observed: 0.236 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.909	α = 90
b = 95.214	β = 97.81
c = 181.532	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
PHASER	phasing
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-11-04

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Science & Technology (DST, India)	India	CRG/2023/004351
Department of Biotechnology (DBT, India)	India	PR32713
Indian Council of Medical Research	India	CAR-2024-01-000140