1PDM Structural Protein date May 19, 2003
title Fitting Of Gp8 Structure Into The Cryoem Reconstruction Of T Bacteriophage T4 Baseplate
authors V.A.Kostyuchenko, P.G.Leiman, P.R.Chipman, S.Kanamaru, M.J.Van R F.Arisaka, V.V.Mesyanzhinov, M.G.Rossmann
compound source
Molecule: Baseplate Structural Protein Gp8
Chain: A, B, C, D, E, F, G, H, I, J, K, L
Synonym: Baseplate Wedge Protein 8
 Organism_scientific: Enterobacteria Phage T4
Organism_taxid: 10665
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 12.00 Å
Gene
Ontology
ChainFunctionProcessComponent
F, A, J, K, E, B, H, C, D, I, G, L


Primary referenceThree-dimensional structure of bacteriophage T4 baseplate., Kostyuchenko VA, Leiman PG, Chipman PR, Kanamaru S, van Raaij MJ, Arisaka F, Mesyanzhinov VV, Rossmann MG, Nat Struct Biol 2003 Sep;10(9):688-93. Epub 2003 Aug 17. PMID:12923574
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (86 Kb) [Save to disk]
  • Biological Unit Coordinates (1pdm.pdb1.gz) 83 Kb
  • CSU: Contacts of Structural Units for 1PDM
  • Likely Quarternary Molecular Structure file(s) for 1PDM
  • Retrieve 1PDM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1PDM from S2C, [Save to disk]
    • View 1PDM 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 1PDM
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1PDM, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1pdma_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1pdmb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1pdmc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1pdmd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1pdme_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1pdmf_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1pdmg_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1pdmh_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1pdmi_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1pdmj_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1pdmk_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1pdml_, region L [Jmol] [rasmolscript] [script source]
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1pdm_A] [1pdm_B] [1pdm_I] [1pdm_K] [1pdm_C] [1pdm_L] [1pdm_J] [1pdm_H] [1pdm] [1pdm_F] [1pdm_E] [1pdm_G] [1pdm_D]
  • SWISS-PROT database: [P19062]
  • Belongs to the gp27/5 t4-baseplate (t4-bp) family according to TCDB.
  • Domain organization of [VG08_BPT4] by SWISSPFAM
    • Other resources with information on 1PDM
  • Community annotation for 1PDM 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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