3PDY Structural Protein date Oct 25, 2010
title Structure Of The Third And Fourth Spectrin Repeats Of The Pl Domain Of Plectin
authors E.Ortega, J.M.De Pereda
compound source
Molecule: Plectin
Chain: A, B
Fragment: Spectrin Repeats 3 And 4 (Unp Residues 653-848)
Synonym: Pcn, Pltn, Hemidesmosomal Protein 1, Hd1, Plectin-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Plec, Plec1
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Modified Pet15b
symmetry Space Group: P 21 21 2
R_factor 0.204 R_Free 0.248
crystal
cell
length a length b length c angle alpha angle beta angle gamma
97.420 119.400 44.580 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.22 Å
ligand EDO, PEG enzyme
note 3PDY is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceThe Structure of the Plakin Domain of Plectin Reveals a Non-canonical SH3 Domain Interacting with Its Fourth Spectrin Repeat., Ortega E, Buey RM, Sonnenberg A, de Pereda JM, J Biol Chem. 2011 Apr 8;286(14):12429-38. Epub 2011 Feb 1. PMID:21288893
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (143 Kb) [Save to disk]
  • Biological Unit Coordinates (3pdy.pdb1.gz) 69 Kb
  • Biological Unit Coordinates (3pdy.pdb2.gz) 69 Kb
  • Biological Unit Coordinates (3pdy.pdb3.gz) 138 Kb
  • LPC: Ligand-Protein Contacts for 3PDY
  • CSU: Contacts of Structural Units for 3PDY
  • Structure Factors (306 Kb)
  • Retrieve 3PDY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3PDY from S2C, [Save to disk]
  • Re-refined 3pdy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3PDY 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 3PDY
  • 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 3PDY, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3pdy_B] [3pdy_A] [3pdy]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3PDY: [SPEC ] by SMART
  • Other resources with information on 3PDY
  • Community annotation for 3PDY 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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