1XD2 Signaling Protein date Sep 03, 2004
title Crystal Structure Of A Ternary Ras:Sos:Rasgdp Complex
authors H.Sondermann, S.M.Soisson, S.Boykevisch, S.S.Yang, D.Bar-Sagi, J.Kuriyan
compound source
Molecule: Transforming Protein P21h-Ras-1
Chain: A
Fragment: Residues 1-166
Synonym: C-H-Ras
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hras, Hras1
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pproexhta

Molecule: Transforming Protein P21h-Ras-1
Chain: B
Fragment: Residues 1-166
Synonym: C-H-Ras
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hras, Hras1
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pproexhta

Molecule: Son Of Sevenless Protein Homolog 1
Chain: C
Fragment: Residues 566-1049, Including Ras Guanine Nucleotide Exchange Factor Fragment;
Synonym: Sos-1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Sos1
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pproexhta
symmetry Space Group: I 4 2 2
R_factor 0.212 R_Free 0.245
crystal
cell
length a length b length c angle alpha angle beta angle gamma
183.703 183.703 177.804 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand GDP, MG, PO4 enzyme
related structures by homologous chain: 1BKD, 1NVW, 1PLJ
Gene
Ontology
ChainFunctionProcessComponent
A, B


C


Primary referenceStructural analysis of autoinhibition in the ras activator son of sevenless., Sondermann H, Soisson SM, Boykevisch S, Yang SS, Bar-Sagi D, Kuriyan J, Cell 2004 Oct 29;119(3):393-405. PMID:15507210
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (138 Kb) [Save to disk]
  • Biological Unit Coordinates (1xd2.pdb1.gz) 133 Kb
  • LPC: Ligand-Protein Contacts for 1XD2
  • CSU: Contacts of Structural Units for 1XD2
  • Likely Quarternary Molecular Structure file(s) for 1XD2
  • Structure Factors (313 Kb)
  • Retrieve 1XD2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1XD2 from S2C, [Save to disk]
  • Re-refined 1xd2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1XD2 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 1XD2
  • 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 1XD2, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1xd2a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1xd2b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1xd2c_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1f1xd2, region D:148-322 [Jmol] [rasmolscript] [script source]
  • Fold representative 1xd2 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1xd2_A] [1xd2] [1xd2_B] [1xd2_C]
  • SWISS-PROT database: [P01112] [Q07889]
  • Domain organization of [RASH_HUMAN] [SOS1_HUMAN] by SWISSPFAM
  • Domains found in 1XD2: [RAS] [RasGEF] [RasGEFN ] by SMART
  • Other resources with information on 1XD2
  • Community annotation for 1XD2 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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