5LPN Endocytosis date Aug 14, 2016
title Structure Of Human Rab10 In Complex With The Bmerb Domain Of
authors A.Rai, A.Oprisko, J.Campos, Y.Fu, T.Friese, A.Itzen, R.S.Goody, M.P E.M.Gazdag
compound source
Molecule: Ras-Related Protein Rab-10
Chain: A, C
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rab10
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Protein-Methionine Sulfoxide Oxidase Mical1
Chain: B
Fragment: Unp Residues 918-1067
Synonym: Molecule Interacting With Casl Protein 1,Mical-1,N Interacting Protein With Calponin Homology And Lim Domains;
Ec: 1.14.13.-
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mical1, Mical, Nical
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.244 R_Free 0.287
length a length b length c angle alpha angle beta angle gamma
58.390 59.000 198.180 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand GNP, MG enzyme Oxidoreductase E.C.1.14.13 BRENDA
A, C


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] (168 Kb) [Save to disk]
  • Biological Unit Coordinates (5lpn.pdb1.gz) 162 Kb
  • LPC: Ligand-Protein Contacts for 5LPN
  • CSU: Contacts of Structural Units for 5LPN
  • Structure Factors (151 Kb)
  • Retrieve 5LPN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5LPN from S2C, [Save to disk]
  • Re-refined 5lpn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5LPN 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 5LPN
  • 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 5lpn from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5lpn] [5lpn_B] [5lpn_C] [5lpn_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5LPN: [DUF3585] [RAB ] by SMART
  • Other resources with information on 5LPN
  • Community annotation for 5LPN at PDBWiki (http://pdbwiki.org)

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