6EKK Transcription date Sep 26, 2017
title Crystal Structure Of Gef Domain Of Dennd 1a In Complex With Rab35-Gdp Bound State.
authors V.Srikannathasan, A.Szykowska, C.Tallant, C.Strain-Damerell, J.K K.Kupinska, S.Mukhopadhyay, M.Gavin, D.Wang, R.Chalk, N.A.Burges C.H.Arrowsmith, A.Edwards, C.Bountra, F.Von Delft, K.Huber
compound source
Molecule: Denn Domain-Containing Protein 1a
Chain: A, B
Synonym: Connecdenn 1,Connecdenn,Protein Fam31a
Engineered: Yes
Other_details: Chain A- Dennd1aa (Uniprot Q8teh3) Chain B- (Uniprot - Q15286);
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dennd1a, Fam31a, Kiaa1608
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell: Sf9
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pfb-Ct10hf-Lic

Molecule: Ras-Related Protein Rab-35
Chain: C, D
Synonym: Gtp-Binding Protein Ray,Ras-Related Protein Rab-1c
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rab35, Rab1c, Ray
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_cell: Escherichia Coli Bl21 De3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pnic28-Bsa4
symmetry Space Group: P 1
R_factor 0.194 R_Free 0.232
length a length b length c angle alpha angle beta angle gamma
55.700 67.990 101.710 80.50 76.80 67.06
method X-Ray Diffractionresolution 1.82 Å
ligand EDO, GDP, SO4 enzyme
A, B

D, C

Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (402 Kb) [Save to disk]
  • Biological Unit Coordinates (6ekk.pdb1.gz) 196 Kb
  • Biological Unit Coordinates (6ekk.pdb2.gz) 202 Kb
  • LPC: Ligand-Protein Contacts for 6EKK
  • CSU: Contacts of Structural Units for 6EKK
  • Structure Factors (2982 Kb)
  • Retrieve 6EKK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6EKK from S2C, [Save to disk]
  • View 6EKK 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 6EKK
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 6ekk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6ekk_D] [6ekk_C] [6ekk_A] [6ekk_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6EKK
  • Community annotation for 6EKK at PDBWiki (http://pdbwiki.org)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science