1EK0 Endocytosis Exocytosis date Mar 06, 2000
title Gppnhp-Bound Ypt51 At 1.48 A Resolution
authors H.Esters, A.J.Scheidig
compound source
Molecule: Protein (Gtp-Binding Protein Ypt51)
Chain: A
Fragment: Gtpase Domain
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21de3
Expression_system_plasmid: Pet19
symmetry Space Group: P 61
length a length b length c angle alpha angle beta angle gamma
62.326 62.326 91.221 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.48 Å
ligand GDP, GNP, MG, MHO, NI enzyme

Primary referenceHigh-resolution crystal structure of S. cerevisiae Ypt51(DeltaC15)-GppNHp, a small GTP-binding protein involved in regulation of endocytosis., Esters H, Alexandrov K, Constantinescu AT, Goody RS, Scheidig AJ, J Mol Biol 2000 Apr 21;298(1):111-21. PMID:10756108
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (39 Kb) [Save to disk]
  • Biological Unit Coordinates (1ek0.pdb1.gz) 34 Kb
  • LPC: Ligand-Protein Contacts for 1EK0
  • CSU: Contacts of Structural Units for 1EK0
  • Likely Quarternary Molecular Structure file(s) for 1EK0
  • Structure Factors (352 Kb)
  • Retrieve 1EK0 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1EK0 from S2C, [Save to disk]
  • Re-refined 1ek0 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1EK0 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 1EK0
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Conformational Epitope Prediction for 1EK0 from the CEP Server.
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1EK0, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ek0a_, region A [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: [1ek0] [1ek0_A]
  • SWISS-PROT database: [P36017]
  • Domain organization of [VPS21_YEAST] by SWISSPFAM
  • Domain found in 1EK0: [RAB ] by SMART
  • Other resources with information on 1EK0
  • Community annotation for 1EK0 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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