2YDL Signaling Protein date Mar 22, 2011
title Crystal Structure Of Sh3c From Cin85
authors J.Bravo, N.Cardenes
compound source
Molecule: Sh3 Domain-Containing Kinase-Binding Protein 1
Chain: A
Fragment: Sh3 C, Residues 270-328
Synonym: Cd2-Binding Protein 3, Cd2bp3, Cbl-Interacting Pro 85 Kda, Human Src Family Kinase-Binding Protein 1, Hsb-1,
Engineered: Yes
Other_details: Third Sh3 Domain
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_vector: Pet21a
symmetry Space Group: P 31 2 1
R_factor 0.20515 R_Free 0.25222
length a length b length c angle alpha angle beta angle gamma
47.828 47.828 70.235 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.05 Å

Primary referenceDistinct Ubiquitin Binding Modes Exhibited by SH3 Domains: Molecular Determinants and Functional Implications., Ortega Roldan JL, Casares S, Ringkjobing Jensen M, Cardenes N, Bravo J, Blackledge M, Azuaga AI, van Nuland NA, PLoS One. 2013 Sep 11;8(9):e73018. doi: 10.1371/journal.pone.0073018. PMID:24039852
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (16 Kb) [Save to disk]
  • Biological Unit Coordinates (2ydl.pdb1.gz) 13 Kb
  • CSU: Contacts of Structural Units for 2YDL
  • Structure Factors (259 Kb)
  • Retrieve 2YDL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2YDL from S2C, [Save to disk]
  • Re-refined 2ydl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2YDL 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 2YDL
  • 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 2YDL, from MSDmotif at EBI
  • Fold representative 2ydl from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ydl] [2ydl_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 2YDL: [SH3 ] by SMART
  • Other resources with information on 2YDL
  • Community annotation for 2YDL at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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