1DDL Virus Rna date Nov 10, 1999
title Desmodium Yellow Mottle Tymovirus
authors S.B.Larson, J.Day, M.A.Canady, A.Greenwood, A.Mcpherson
compound source
Molecule: Rna (5'-R(Pupupupupupupu)-3')
Chain: D
Fragment: Viral Rna Fragment
Engineered: Yes
Synthetic: Yes

Molecule: Rna (5'-R(Pupu)-3')
Chain: E
Fragment: Viral Rna Fragment
Engineered: Yes

Synthetic: Yes

Molecule: Desmodium Yellow Mottle Virus
Chain: A, B, C
Fragment: Viral Coat Protein

Organism_scientific: Desmodium Yellow Mottle Virus
Organism_taxid: 70821
symmetry Space Group: P 42 3 2
R_factor 0.151 R_Free 0.159
crystal
cell
length a length b length c angle alpha angle beta angle gamma
348.546 348.546 348.546 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
note 1DDL is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


Primary referenceRefined structure of desmodium yellow mottle tymovirus at 2.7 A resolution., Larson SB, Day J, Canady MA, Greenwood A, McPherson A, J Mol Biol 2000 Aug 18;301(3):625-42. PMID:10966774
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (99 Kb) [Save to disk]
  • Biological Unit Coordinates (1ddl.pdb1.gz) 5508 Kb
  • CSU: Contacts of Structural Units for 1DDL
  • Likely Quarternary Molecular Structure file(s) for 1DDL
  • Structure Factors (1383 Kb)
  • Retrieve 1DDL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DDL from S2C, [Save to disk]
  • Re-refined 1ddl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1DDL 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 1DDL
  • VIPERdb: visual, structural and computational analysis of 1DDL
  • 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
  • 3D motif for 1DDL, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ddla_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1ddlb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1ddlc_, region C [Jmol] [rasmolscript] [script source]
  • 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: [1ddl_B] [1ddl_D] [1ddl_C] [1ddl] [1ddl_A] [1ddl_E]
  • SWISS-PROT database: [O89511]
  • Domain organization of [O89511_9VIRU] by SWISSPFAM
  • Other resources with information on 1DDL
  • Community annotation for 1DDL 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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