5KHO Signaling Protein date Jun 15, 2016
title Rasip1 Ra Domain In Complex With Rap1b
authors A.R.Gingras
compound source
Molecule: Ras-Interacting Protein 1
Chain: A, B
Synonym: Rain
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rasip1
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)

Molecule: Ras-Related Protein Rap-1b
Chain: C, D
Synonym: Gtp-Binding Protein Smg P21b
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rap1b, Oksw-Cl.11
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
symmetry Space Group: P 21 21 2
R_factor 0.205 R_Free 0.286
crystal
cell
length a length b length c angle alpha angle beta angle gamma
101.540 154.760 38.800 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.78 Å
ligand GNP, GOL, MG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


D, C


Primary referenceStructural Basis of Dimeric Rasip1 RA Domain Recognition of the Ras Subfamily of GTP-Binding Proteins., Gingras AR, Puzon-McLaughlin W, Bobkov AA, Ginsberg MH, Structure. 2016 Dec 6;24(12):2152-2162. doi: 10.1016/j.str.2016.10.001. Epub 2016, Nov 10. PMID:27839947
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (91 Kb) [Save to disk]
  • Biological Unit Coordinates (5kho.pdb1.gz) 84 Kb
  • LPC: Ligand-Protein Contacts for 5KHO
  • CSU: Contacts of Structural Units for 5KHO
  • Structure Factors (343 Kb)
  • Retrieve 5KHO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5KHO from S2C, [Save to disk]
  • Re-refined 5kho structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5KHO 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 5KHO
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5kho_C] [5kho_D] [5kho_A] [5kho] [5kho_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5KHO: [RA] [RAS ] by SMART
  • Other resources with information on 5KHO
  • Community annotation for 5KHO at PDBWiki (http://pdbwiki.org)

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