1F7U Ligase Rna date Jun 28, 2000
title Crystal Structure Of The Arginyl-Trna Synthetase Complexed W Trna(Arg) And L-Arg
authors B.Delagoutte, D.Moras, J.Cavarelli
compound source
Molecule: Trna(Arg)
Chain: B
Engineered: Yes
Synthetic: Yes
Other_details: This Sequence Occurs Naturally In Yeast Sacc Cerevisae;

Molecule: Arginyl-Trna Synthetase
Chain: A
Synonym: Cytoplasmic Arginine-Trna Ligase, Argrs
Ec: 6.1.1.19
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ptrc99
symmetry Space Group: P 21 21 2
R_factor 0.190 R_Free 0.233
crystal
cell
length a length b length c angle alpha angle beta angle gamma
129.646 107.472 71.379 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand 1MA, 1MG, 2MG, 5MC, 5MU, ARG, H2U, M2G, PSU, SO4 enzyme Ligase E.C.6.1.1.19 BRENDA
related structures by homologous chain: 1BS2
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referencetRNA aminoacylation by arginyl-tRNA synthetase: induced conformations during substrates binding., Delagoutte B, Moras D, Cavarelli J, EMBO J 2000 Nov 1;19(21):5599-610. PMID:11060012
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (150 Kb) [Save to disk]
  • Biological Unit Coordinates (1f7u.pdb1.gz) 144 Kb
  • LPC: Ligand-Protein Contacts for 1F7U
  • CSU: Contacts of Structural Units for 1F7U
  • Likely Quarternary Molecular Structure file(s) for 1F7U
  • Structure Factors (431 Kb)
  • Retrieve 1F7U in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1F7U from S2C, [Save to disk]
  • Re-refined 1f7u structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1F7U in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 1F7U
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1F7U, from MSDmotif at EBI
  • Structure summary from SCOR (Structural Classification of RNA)
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1f7ua2, region A:136-483 [Jmol] [rasmolscript] [script source]
        - Domain d1f7ua3, region A:2-135 [Jmol] [rasmolscript] [script source]
        - Domain d1f7ua1, region A:484-607 [Jmol] [rasmolscript] [script source]
  • Fold representative 1f7u from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1f7u_A] [1f7u] [1f7u_B]
  • SWISS-PROT database: [Q05506]
  • Domain organization of [SYRC_YEAST] by SWISSPFAM
  • Domains found in 1F7U: [Arg_tRNA_synt_N] [DALR_1 ] by SMART
  • Other resources with information on 1F7U
  • Community annotation for 1F7U at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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