4CYM Transport Protein date Apr 13, 2014
title Complex Of Human Varp-Ankrd1 With Rab32-Gppcp
authors I.Perez-Dorado, I.B.Schaefer, A.J.Mccoy, D.J.Owen, P.R.Evans
compound source
Molecule: Ras-Related Protein Rab-32
Chain: A, B, C
Synonym: Rab32
Ec: 3.6.5.2
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Rosetta 2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-6p-1

Molecule: Ankyrin Repeat Domain-Containing Protein 27
Chain: D, E, F
Fragment: First Ankyrin Repeat-Containing Domain, Residues
Synonym: Vps9-Domain Ankyrin Repeat Protein, Vps9 Domain-Co P;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Rosetta 2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-6p-1
symmetry Space Group: P 32 2 1
R_factor 0.19205 R_Free 0.24565
crystal
cell
length a length b length c angle alpha angle beta angle gamma
144.445 144.445 135.680 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.80 Å
ligand GCP, MG enzyme Hydrolase E.C.3.6.5.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


Primary referenceVARP Is Recruited on to Endosomes by Direct Interaction with Retromer, Where Together They Function in Export to the Cell Surface., Hesketh GG, Perez-Dorado I, Jackson LP, Wartosch L, Schafer IB, Gray SR, McCoy AJ, Zeldin OB, Garman EF, Harbour ME, Evans PR, Seaman MN, Luzio JP, Owen DJ, Dev Cell. 2014 May 21. pii: S1534-5807(14)00230-5. doi:, 10.1016/j.devcel.2014.04.010. PMID:24856514
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (179 Kb) [Save to disk]
  • Biological Unit Coordinates (4cym.pdb1.gz) 115 Kb
  • Biological Unit Coordinates (4cym.pdb2.gz) 114 Kb
  • Biological Unit Coordinates (4cym.pdb3.gz) 114 Kb
  • Biological Unit Coordinates (4cym.pdb4.gz) 59 Kb
  • Biological Unit Coordinates (4cym.pdb5.gz) 58 Kb
  • Biological Unit Coordinates (4cym.pdb6.gz) 59 Kb
  • LPC: Ligand-Protein Contacts for 4CYM
  • CSU: Contacts of Structural Units for 4CYM
  • Structure Factors (2159 Kb)
  • Retrieve 4CYM in mmCIF format [Save to disk]
  • Re-refined 4cym structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4CYM 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 4CYM
  • 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 4CYM, from MSDmotif at EBI
  • Fold representative 4cym from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4cym_C] [4cym_A] [4cym_F] [4cym_E] [4cym_B] [4cym] [4cym_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4CYM: [ANK] [RAB ] by SMART
  • Other resources with information on 4CYM
  • Community annotation for 4CYM at PDBWiki (http://pdbwiki.org)

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