2VRF Protein Binding date Mar 31, 2008
title Crystal Structure Of The Human Beta-2-Syntrophin Pdz Domain
authors Z.Sun, A.K.Roos, A.C.W.Pike, E.S.Pilka, C.Cooper, J.M.Elkins, J.Mu C.H.Arrowsmith, D.Doyle, A.Edwards, F.Von Delft, C.Bountra, U.Op
compound source
Molecule: Beta-2-Syntrophin
Chain: A, B, C, D
Fragment: Pdz Domain, Residues 112-200
Synonym: 59 Kda Dystrophin-Associated Protein A1 Basic Comp Syntrophin-3, Snt3, Syntrophin-Like, Sntl;
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_variant: R3-Prare2
Expression_system_plasmid: Pnic28-Bsa4
symmetry Space Group: P 1 21 1
R_factor 0.184 R_Free 0.247
crystal
cell
length a length b length c angle alpha angle beta angle gamma
56.687 29.503 128.382 90.00 95.78 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand EDO enzyme
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (69 Kb) [Save to disk]
  • Biological Unit Coordinates (2vrf.pdb1.gz) 17 Kb
  • Biological Unit Coordinates (2vrf.pdb2.gz) 17 Kb
  • Biological Unit Coordinates (2vrf.pdb3.gz) 17 Kb
  • Biological Unit Coordinates (2vrf.pdb4.gz) 16 Kb
  • Biological Unit Coordinates (2vrf.pdb5.gz) 32 Kb
  • Biological Unit Coordinates (2vrf.pdb6.gz) 31 Kb
  • LPC: Ligand-Protein Contacts for 2VRF
  • CSU: Contacts of Structural Units for 2VRF
  • Likely Quarternary Molecular Structure file(s) for 2VRF
  • Structure Factors (375 Kb)
  • Retrieve 2VRF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VRF from S2C, [Save to disk]
  • Re-refined 2vrf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VRF 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 2VRF
  • 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 2VRF, from MSDmotif at EBI
  • Fold representative 2vrf from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vrf] [2vrf_B] [2vrf_A] [2vrf_D] [2vrf_C]
  • SWISS-PROT database: [Q13425]
  • Domain organization of [SNTB2_HUMAN] by SWISSPFAM
  • Domain found in 2VRF: [PDZ ] by SMART
  • Other resources with information on 2VRF
  • Community annotation for 2VRF 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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