1G16 Signaling Protein,Endocytosis Exocytosis date Oct 10, 2000
title Crystal Structure Of Sec4-Gdp
authors C.Stroupe, A.T.Brunger
compound source
Molecule: Ras-Related Protein Sec4
Chain: A, B, C, D
Fragment: Residues 18-187
Synonym: Gtp-Binding Protein Sec4
Engineered: Yes
 Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-4t-1
symmetry Space Group: P 1
R_factor 0.276 R_Free 0.296
crystal
cell
length a length b length c angle alpha angle beta angle gamma
56.007 56.379 59.374 95.25 101.68 116.20
method X-Ray Diffractionresolution 1.80 Å
ligand CO, GDP, MSE enzyme
related structures by homologous chain: 1G17
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceCrystal structures of a Rab protein in its inactive and active conformations., Stroupe C, Brunger AT, J Mol Biol 2000 Dec 8;304(4):585-98. PMID:11099382
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (121 Kb) [Save to disk]
  • Biological Unit Coordinates (1g16.pdb1.gz) 114 Kb
  • LPC: Ligand-Protein Contacts for 1G16
  • CSU: Contacts of Structural Units for 1G16
  • Likely Quarternary Molecular Structure file(s) for 1G16
  • Structure Factors (972 Kb)
  • Retrieve 1G16 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1G16 from S2C, [Save to disk]
  • Re-refined 1g16 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1G16 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 1G16
  • 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 1G16, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1g16a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1g16b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1g16c_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1g16d_, region D [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: [1g16_B] [1g16_D] [1g16_A] [1g16_C] [1g16]
  • SWISS-PROT database: [P07560]
  • Domain organization of [SEC4_YEAST] by SWISSPFAM
  • Domain found in 1G16: [RAB ] by SMART
    • Other resources with information on 1G16
  • Community annotation for 1G16 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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