[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleThe active site of aspartyl-tRNA synthetase: Structural studies of the adenylation reaction and flexibility of residues.
Journal, issue, pagesTo Be Published
Publish dateAug 19, 2025 (structure data deposition date)
AuthorsSharma, V.K. / Manickam, Y. / Sharma, A.
External linksSearch PubMed
MethodsX-ray diffraction
Resolution2.01 - 2.68 Å
Structure data

PDB-9we8:
Plasmodium vivax aspartyl-tRNA synthetase (PvDRS) complexed with the non-hydrolysable ATP analogue AMP-PCP (ACP)
Method: X-RAY DIFFRACTION / Resolution: 2.395 Å

PDB-9we9:
Plasmodium vivax aspartyl-tRNA synthetase in complex with L-Asp, Lanthanide, MOPSO and Butanetriol
Method: X-RAY DIFFRACTION / Resolution: 2.402 Å

PDB-9wea:
Plasmodium vivax aspartyl-tRNA synthetase in complex with AMP, PO4, MOPS and Alcohols
Method: X-RAY DIFFRACTION / Resolution: 2.301 Å

PDB-9web:
Plasmodium vivax aspartyl-tRNA synthetase in complex with AMP, Pyrophosphate, MOPSO and Hexanetriol
Method: X-RAY DIFFRACTION / Resolution: 2.541 Å

PDB-9wec:
Plasmodium vivax aspartyl-tRNA synthetase in complex with AMP, Divalent metals, MOPSO and Butanetriol
Method: X-RAY DIFFRACTION / Resolution: 2.391 Å

PDB-9wed:
Plasmodium vivax aspartyl-tRNA synthetase in complex with AMP, Asp-AMP, Partially occupied ASP, Mg ion and Butanetriol
Method: X-RAY DIFFRACTION / Resolution: 2.158 Å

PDB-9wee:
Plasmodium vivax aspartyl-tRNA synthetase in complex with Asp-AMP and SO4
Method: X-RAY DIFFRACTION / Resolution: 2.32 Å

PDB-9wef:
Plasmodium vivax aspartyl-tRNA synthetase in complex with AMS and SO4
Method: X-RAY DIFFRACTION / Resolution: 2.402 Å

PDB-9weg:
Plasmodium vivax aspartyl-tRNA synthetase in complex with AMS, Mg ion, Iodides and Pentaethylene glycol
Method: X-RAY DIFFRACTION / Resolution: 2.228 Å

PDB-9weh:
Plasmodium vivax aspartyl-tRNA synthetase in complex with Asp-AMS, SO4, MOPSO and Butanetriol
Method: X-RAY DIFFRACTION / Resolution: 2.094 Å

PDB-9wei:
Plasmodium vivax aspartyl-tRNA synthetase in complex with Asp-AMS, Divalent metals, MOPSO and Pentanediol
Method: X-RAY DIFFRACTION / Resolution: 2.53 Å

PDB-9wej:
Plasmodium vivax aspartyl-tRNA synthetase in complex with Asp-AMS, Ytterbium, MOPSO and Hexanetriol
Method: X-RAY DIFFRACTION / Resolution: 2.68 Å

PDB-9wek:
Plasmodium vivax aspartyl-tRNA synthetase in complex with Asp-AMS in the absence of Mg ions
Method: X-RAY DIFFRACTION / Resolution: 2.01 Å

PDB-9wel:
Plasmodium vivax aspartyl-tRNA synthetase in complex with Asp-AMS, Mg ion, Ethylene glycols and Unit cell contraction due to data collected outside the cryo loop
Method: X-RAY DIFFRACTION / Resolution: 2.201 Å

PDB-9wem:
Plasmodium vivax aspartyl-tRNA synthetase in combination with Asp-AMS, Mg ion, MOPS and PGE
Method: X-RAY DIFFRACTION / Resolution: 2.128 Å

Chemicals

ChemComp-ACP:
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / AMP-PCP, energy-carrying molecule analogue*YM

ChemComp-GOL:
GLYCEROL

ChemComp-HEZ:
HEXANE-1,6-DIOL

ChemComp-HOH:
WATER

ChemComp-ASP:
ASPARTIC ACID

ChemComp-YB:
YTTERBIUM (III) ION

ChemComp-CL:
Unknown entry

ChemComp-0V1:
(2~{S})-butane-1,2,4-triol

ChemComp-6BX:
(2S)-2-hydroxy-3-(morpholin-4-yl)propane-1-sulfonic acid

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

ChemComp-PO4:
PHOSPHATE ION

ChemComp-MPO:
3[N-MORPHOLINO]PROPANE SULFONIC ACID / pH buffer*YM

ChemComp-PGO:
S-1,2-PROPANEDIOL

ChemComp-PDO:
1,3-PROPANDIOL

ChemComp-6BY:
(2R)-2-hydroxy-3-(morpholin-4-yl)propane-1-sulfonic acid

ChemComp-PPV:
PYROPHOSPHATE

ChemComp-1JW:
(2S)-hexane-1,2,6-triol

ChemComp-ZN:
Unknown entry

ChemComp-MN:
Unknown entry

ChemComp-CO:
Unknown entry

ChemComp-AMO:
ASPARTYL-ADENOSINE-5'-MONOPHOSPHATE

ChemComp-MG:
Unknown entry

ChemComp-SO4:
SULFATE ION

ChemComp-LMS:
[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDRO-2-FURANYL]METHYL SULFAMATE

ChemComp-EPE:
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / pH buffer*YM

ChemComp-IOD:
IODIDE ION

ChemComp-1PE:
PENTAETHYLENE GLYCOL / precipitant*YM

ChemComp-DSZ:
5'-O-(L-alpha-aspartylsulfamoyl)adenosine

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER

ChemComp-PGE:
TRIETHYLENE GLYCOL

ChemComp-9JE:
pentane-1,5-diol

ChemComp-BME:
BETA-MERCAPTOETHANOL

Source
  • plasmodium vivax (malaria parasite P. vivax)
KeywordsLIGASE / AMINOACYLATION / AMINOACYL-TRNA SYNTHETASE / TRNA-BINDING / ATP-BINDING / MALARIA / INHIBITOR

+
About Yorodumi Papers

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more