9WEH | pdb_00009weh

Plasmodium vivax aspartyl-tRNA synthetase in complex with Asp-AMS, SO4, MOPSO and Butanetriol

PDB DOI: https://doi.org/10.2210/pdb9WEH/pdb

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

Deposited: 2025-08-19 Released: 2026-09-02
Deposition Author(s): Manickam, Y., Sharma, V.K., Bagale, S., Pradeepkumar, P.I., Sharma, A.
Funding Organization(s): Department of Biotechnology (DBT, India), Indian Council of Medical Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free:
0.211 (Depositor), 0.212 (DCC)
R-Value Work:
0.175 (Depositor), 0.182 (DCC)
R-Value Observed:
0.177 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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Literature

The active site of aspartyl-tRNA synthetase: Structural studies of the adenylation reaction and flexibility of residues.

Sharma, V.K., Manickam, Y., Sharma, A.

To be published.

Macromolecule Content

Total Structure Weight: 126.74 kDa
Atom Count: 9,055
Modeled Residue Count: 1,006
Deposited Residue Count: 1,072
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
aspartate--tRNA ligase	A, B	536	Plasmodium vivax	Mutation(s): 0 Gene Names: PVC01_020016700, PVW1_020019400 EC: 6.1.1.12
UniProt
Find proteins for A0A1G4H6Y1 (Plasmodium vivax) Explore A0A1G4H6Y1 Go to UniProtKB: A0A1G4H6Y1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1G4H6Y1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DSZ (Subject of Investigation/LOI) Query on DSZ Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain J [auth B]	C [auth A], J [auth B]	5'-O-(L-alpha-aspartylsulfamoyl)adenosine C₁₄ H₁₉ N₇ O₉ S KMRBRMHHDAUXAY-UFIIOMENSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
6BX (Subject of Investigation/LOI) Query on 6BX Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	(2S)-2-hydroxy-3-(morpholin-4-yl)propane-1-sulfonic acid C₇ H₁₅ N O₅ S NUFBIAUZAMHTSP-ZETCQYMHSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
PGE (Subject of Investigation/LOI) Query on PGE Download:Ideal Coordinates CCD File SDF format, chain R [auth B] MOL2 format, chain R [auth B] mmCIF format, chain R [auth B]	R [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain R [auth B] Interactions & Density Focus chain R [auth B]
0V1 (Subject of Investigation/LOI) Query on 0V1 Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain G [auth A] SDF format, chain E [auth A] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A]	E [auth A], G [auth A], M [auth B], N [auth B]	(2~{S})-butane-1,2,4-triol C₄ H₁₀ O₃ ARXKVVRQIIOZGF-BYPYZUCNSA-N		Interactions Focus chain E [auth A] Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B]
PEG (Subject of Investigation/LOI) Query on PEG Download:Ideal Coordinates CCD File SDF format, chain P [auth B] MOL2 format, chain P [auth B] mmCIF format, chain P [auth B]	P [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain P [auth B] Interactions & Density Focus chain P [auth B]
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain D [auth A] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain D [auth A] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain D [auth A]	D [auth A], K [auth B], L [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain K [auth B] Focus chain L [auth B]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain O [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain O [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain O [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A], O [auth B], Q [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain Q [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain Q [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free: 0.211 (Depositor), 0.212 (DCC)
R-Value Work: 0.175 (Depositor), 0.182 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.779	α = 90
b = 139.779	β = 90
c = 274.11	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-02

Deposition Author(s):

Pradeepkumar, P.I.

Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	PR32713
Indian Council of Medical Research	India	CAR grant 2024-000140

Revision History (Full details and data files)

Version 1.0: 2026-09-02
Type: Initial release

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