9WEC | pdb_00009wec

Plasmodium vivax aspartyl-tRNA synthetase in complex with AMP, Divalent metals, MOPSO and Butanetriol

PDB DOI: https://doi.org/10.2210/pdb9WEC/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): Sharma, V.K., Manickam, Y., Sharma, A.
Funding Organization(s): Department of Biotechnology (DBT, India), Indian Council of Medical Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free:
0.224 (Depositor), 0.236 (DCC)
R-Value Work:
0.192 (Depositor), 0.206 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

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: 126.27 kDa
Atom Count: 8,520
Modeled Residue Count: 1,008
Deposited Residue Count: 1,072
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

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
AMP (Subject of Investigation/LOI) Query on AMP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain O [auth B] MOL2 format, chain C [auth A] MOL2 format, chain O [auth B] mmCIF format, chain C [auth A] mmCIF format, chain O [auth B]	C [auth A], O [auth B]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain O [auth B] Interactions & Density Focus chain C [auth A] Focus chain O [auth B]
6BY (Subject of Investigation/LOI) Query on 6BY Download:Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	(2R)-2-hydroxy-3-(morpholin-4-yl)propane-1-sulfonic acid C₇ H₁₅ N O₅ S NUFBIAUZAMHTSP-SSDOTTSWSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
0V1 (Subject of Investigation/LOI) Query on 0V1 Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain N [auth A] SDF format, chain U [auth B] SDF format, chain V [auth B] MOL2 format, chain L [auth A] MOL2 format, chain N [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] mmCIF format, chain L [auth A] mmCIF format, chain N [auth A] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B]	L [auth A], N [auth A], U [auth B], V [auth B]	(2~{S})-butane-1,2,4-triol C₄ H₁₀ O₃ ARXKVVRQIIOZGF-BYPYZUCNSA-N		Interactions Focus chain L [auth A] Focus chain N [auth A] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain L [auth A] Focus chain N [auth A] Focus chain U [auth B] Focus chain V [auth B]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B]	D [auth A], E [auth A], P [auth B], Q [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain P [auth B] Focus chain Q [auth B]
CO Query on CO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain R [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain R [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain R [auth B]	G [auth A], H [auth A], R [auth B]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain R [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain R [auth B]
MN Query on MN 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]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain K [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain K [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain K [auth A]	I [auth A], J [auth A], K [auth A], S [auth B], T [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain S [auth B] Focus chain T [auth B]