3QBV Protein Binding Signaling Protein date Jan 14, 2011
title Structure Of Designed Orthogonal Interaction Between Cdc42 A Nucleotide Exchange Domains Of Intersectin
authors G.T.Kapp, A.Remenyi, W.A.Lim, T.Kortemme
compound source
Molecule: Cell Division Control Protein 42 Homolog
Chain: A, C
Fragment: Unp Residues 1-178
Synonym: G25k Gtp-Binding Protein
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cdc42
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Rosetta2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgkc006

Molecule: Intersectin-1
Chain: B, D
Fragment: Dh And Ph Domains (Unp Residues 1229-1571)
Synonym: Sh3 Domain-Containing Protein 1a, Sh3p17
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Itsn1, Itsn, Sh3d1a
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Rosetta2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgki009
symmetry Space Group: P 1 21 1
R_factor 0.241 R_Free 0.284
crystal
cell
length a length b length c angle alpha angle beta angle gamma
85.460 80.062 94.591 90.00 108.23 90.00
method X-Ray Diffractionresolution 2.65 Å
ligand GDP enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, C
  • ubiquitin protein ligase act...


  • D, B


    Primary referenceControl of protein signaling using a computationally designed GTPase/GEF orthogonal pair., Kapp GT, Liu S, Stein A, Wong DT, Remenyi A, Yeh BJ, Fraser JS, Taunton J, Lim WA, Kortemme T, Proc Natl Acad Sci U S A. 2012 Mar 7. PMID:22403064
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (301 Kb) [Save to disk]
  • Biological Unit Coordinates (3qbv.pdb1.gz) 146 Kb
  • Biological Unit Coordinates (3qbv.pdb2.gz) 146 Kb
  • LPC: Ligand-Protein Contacts for 3QBV
  • CSU: Contacts of Structural Units for 3QBV
  • Structure Factors (258 Kb)
  • Retrieve 3QBV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3QBV from S2C, [Save to disk]
  • Re-refined 3qbv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3QBV 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 3QBV
  • 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 3QBV, from MSDmotif at EBI
  • Fold representative 3qbv from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3qbv_B] [3qbv_D] [3qbv] [3qbv_A] [3qbv_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3QBV: [PH] [RHO] [RhoGEF ] by SMART
  • Other resources with information on 3QBV
  • Community annotation for 3QBV at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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