1PD1 Transport Protein date May 18, 2003
title Crystal Structure Of The Copii Coat Subunit, Sec24, Complexe Peptide Containing The Dxe Cargo Sorting Signal Of Yeast Sy
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: Dxe Cargo Sorting Signal Peptide Of Yeast Sys1 Pr
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 0.203 R_Free 0.256
crystal
cell
length a length b length c angle alpha angle beta angle gamma
93.949 93.949 199.927 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.60 Å
ligand ZN enzyme
related structures by homologous chain: 1PCX, 1PD0
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] (126 Kb) [Save to disk]
  • Biological Unit Coordinates (1pd1.pdb1.gz) 120 Kb
  • LPC: Ligand-Protein Contacts for 1PD1
  • CSU: Contacts of Structural Units for 1PD1
  • Likely Quarternary Molecular Structure file(s) for 1PD1
  • Retrieve 1PD1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1PD1 from S2C, [Save to disk]
  • View 1PD1 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 1PD1
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1PD1, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1pd1a2, region A:133-215,A:553-646 [Jmol] [rasmolscript] [script source]
        - Domain d1pd1a5, region A:216-300 [Jmol] [rasmolscript] [script source]
        - Domain d1pd1a3, region A:301-552 [Jmol] [rasmolscript] [script source]
        - Domain d1pd1a1, region A:647-753 [Jmol] [rasmolscript] [script source]
        - Domain d1pd1a4, region A:754-926 [Jmol] [rasmolscript] [script source]
        - Domain d1h1pd1, region D:175-309 [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: [1pd1] [1pd1_B] [1pd1_A]
  • SWISS-PROT database: [P40482]
  • Domain organization of [SEC24_YEAST] by SWISSPFAM
  • Other resources with information on 1PD1
  • Community annotation for 1PD1 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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