1PD0 Transport Protein date May 18, 2003
title Crystal Structure Of The Copii Coat Subunit, Sec24, Complexe Peptide From The Snare Protein Sed5 (Yeast Syntaxin-5)
authors E.Mossessova, L.C.Bickford, J.Goldberg
compound source
Molecule: Protein Transport Protein Sec24
Chain: A
Synonym: Abnormal Nuclear Morphology 1
Other_details: Sec24 Fragment Lacking N-Terminal Residues 1
 Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Copii-Binding Peptide Of The Integral Membrane Pr Sed5;
Chain: B
Engineered: Yes
Synthetic: Yes
Other_details: The Peptide Was Chemically Synthesized. The Of The Peptide Is Naturally Found In Saccharomyces Cerevisi
symmetry Space Group: P 32 2 1
R_factor 0.206 R_Free 0.254
crystal
cell
length a length b length c angle alpha angle beta angle gamma
94.527 94.527 197.935 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.60 Å
ligand ZN enzyme
related structures by homologous chain: 1M2V, 1PD1
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceSNARE selectivity of the COPII coat., Mossessova E, Bickford LC, Goldberg J, Cell. 2003 Aug 22;114(4):483-95. PMID:12941276
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (125 Kb) [Save to disk]
  • Biological Unit Coordinates (1pd0.pdb1.gz) 120 Kb
  • LPC: Ligand-Protein Contacts for 1PD0
  • CSU: Contacts of Structural Units for 1PD0
  • Likely Quarternary Molecular Structure file(s) for 1PD0
  • Retrieve 1PD0 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1PD0 from S2C, [Save to disk]
    • View 1PD0 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 1PD0
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1PD0, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1pd0a2, region A:133-215,A:553-646 [Jmol] [rasmolscript] [script source]
        - Domain d1pd0a5, region A:216-300 [Jmol] [rasmolscript] [script source]
        - Domain d1pd0a3, region A:301-552 [Jmol] [rasmolscript] [script source]
        - Domain d1pd0a1, region A:647-753 [Jmol] [rasmolscript] [script source]
        - Domain d1pd0a4, region A:754-926 [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: [1pd0_B] [1pd0] [1pd0_A]
  • SWISS-PROT database: [P40482] [Q01590]
  • Domain organization of [SEC24_YEAST] [SED5_YEAST] by SWISSPFAM
    • Other resources with information on 1PD0
  • Community annotation for 1PD0 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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