1YZK Protein Transport date Feb 28, 2005
title Gppnhp Bound Rab11 Gtpase
authors S.Eathiraj, X.Pan, C.Ritacco, D.G.Lambright
compound source
Molecule: Ras-Related Protein Rab-11a
Chain: A
Synonym: Rab-11, Yl8
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rab11a, Rab11
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 (De3) Codon Plus-Ril Cells
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Modified Pet15b
symmetry Space Group: I 4 2 2
R_factor 0.178 R_Free 0.228
length a length b length c angle alpha angle beta angle gamma
73.946 73.946 148.197 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand GNP, MG enzyme

Primary referenceStructural basis of family-wide Rab GTPase recognition by rabenosyn-5., Eathiraj S, Pan X, Ritacco C, Lambright DG, Nature 2005 Jul 21;436(7049):415-9. PMID:16034420
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (37 Kb) [Save to disk]
  • Biological Unit Coordinates (1yzk.pdb1.gz) 32 Kb
  • LPC: Ligand-Protein Contacts for 1YZK
  • CSU: Contacts of Structural Units for 1YZK
  • Likely Quarternary Molecular Structure file(s) for 1YZK
  • Structure Factors (162 Kb)
  • Retrieve 1YZK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YZK from S2C, [Save to disk]
  • Re-refined 1yzk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1YZK 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 1YZK
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1YZK, from MSDmotif at EBI
  • Fold representative 1yzk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1yzk] [1yzk_A]
  • SWISS-PROT database: [P62491]
  • Domain organization of [RB11A_HUMAN] by SWISSPFAM
  • Domain found in 1YZK: [RAB ] by SMART
  • Other resources with information on 1YZK
  • Community annotation for 1YZK 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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