5SZK Endocytosis date Aug 14, 2016
title Structure Of Human N-Terminally Engineered Rab1b In Complex Bmerb Domain Of Mical-Cl
authors A.Rai, A.Oprisko, J.Campos, Y.Fu, T.Friese, A.Itzen, R.S.Goody, E.M M.P.Mueller
compound source
Molecule: Mical C-Terminal-Like Protein
Chain: A
Synonym: Erk2-Binding Testicular Protein 1,Ebitein-1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Micalcl
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ras-Related Protein Rab-1b
Chain: B
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rab1b
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 2 2 21
R_factor 0.208 R_Free 0.261
crystal
cell
length a length b length c angle alpha angle beta angle gamma
62.230 117.030 139.430 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand GNP, MG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referencebMERB domains are bivalent Rab8 family effectors evolved by gene duplication., Rai A, Oprisko A, Campos J, Fu Y, Friese T, Itzen A, Goody RS, Gazdag EM, Muller MP, Elife. 2016 Aug 23;5. pii: e18675. doi: 10.7554/eLife.18675. PMID:27552051
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (118 Kb) [Save to disk]
  • Biological Unit Coordinates (5szk.pdb1.gz) 112 Kb
  • LPC: Ligand-Protein Contacts for 5SZK
  • CSU: Contacts of Structural Units for 5SZK
  • Structure Factors (114 Kb)
  • Retrieve 5SZK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5SZK from S2C, [Save to disk]
  • Re-refined 5szk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5SZK 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 5SZK
  • 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
  • Fold representative 5szk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5szk_B] [5szk] [5szk_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5SZK: [DUF3585] [RAB ] by SMART
  • Other resources with information on 5SZK
  • Community annotation for 5SZK at PDBWiki (http://pdbwiki.org)

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