3OB1 Ligase Signaling Protein date Aug 06, 2010
title Crystal Structure Of C-Cbl Tkb Domain In Complex With Double Phosphorylated Spry2 Peptide
authors Q.Sun, J.Sivaraman
compound source
Molecule: 12-Meric Peptide From Protein Sprouty Homolog 2
Chain: A
Fragment: Residues 49-60
Synonym: Spry-2
Engineered: Yes
Other_details: Double Phosphorylated Spry2 Peptide
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: Synthetic Peptide

Molecule: E3 Ubiquitin-Protein Ligase Cbl
Chain: B
Fragment: C-Cbl Tkb Domain, Residues 25-351
Synonym: Signal Transduction Protein Cbl, Proto-Oncogene C- Casitas B-Lineage Lymphoma Proto-Oncogene, Ring Finger Prot
Ec: 6.3.2.-
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_vector_type: Plasmid
Expression_system_plasmid: Pgex-4t-1
symmetry Space Group: P 6
R_factor 0.181 R_Free 0.223
length a length b length c angle alpha angle beta angle gamma
122.092 122.092 55.689 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.20 Å
ligand PTR, TPO enzyme Ligase E.C.6.3.2 BRENDA

Primary referenceAdditional serine/threonine phosphorylation reduces binding affinity but preserves interface topography of substrate proteins to the c-Cbl TKB domain., Sun Q, Jackson RA, Ng C, Guy GR, Sivaraman J, PLoS One. 2010 Sep 22;5(9):e12819. PMID:20877636
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (108 Kb) [Save to disk]
  • Biological Unit Coordinates (3ob1.pdb1.gz) 103 Kb
  • LPC: Ligand-Protein Contacts for 3OB1
  • CSU: Contacts of Structural Units for 3OB1
  • Structure Factors (363 Kb)
  • Retrieve 3OB1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3OB1 from S2C, [Save to disk]
  • Re-refined 3ob1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3OB1 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 3OB1
  • 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 3OB1, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1b3ob1, region B:10-111,B:232-499 [Jmol] [rasmolscript] [script source]
        - Domain d1c3ob1, region B:2-152 [Jmol] [rasmolscript] [script source]
        - Domain d1k3ob1, region B:81-209 [Jmol] [rasmolscript] [script source]
  • Fold representative 3ob1 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ob1_B] [3ob1_A] [3ob1]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3OB1
  • Community annotation for 3OB1 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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