5YPR Protein Binding date Nov 02, 2017
title Crystal Structure Of Psd-95 Sh3-Gk Domain In Complex With A Synthesized Inhibitor
authors J.Zhu, Q.Zhou, Y.Shang, Z.Weng, R.Zhu, M.Zhang
compound source
Molecule: Disks Large Homolog 4
Chain: A
Synonym: Postsynaptic Density Protein 95,Psd-95,Synapse-Ass Protein 90,Sap90;
Engineered: Yes
Organism_scientific: Rattus Norvegicus
Organism_common: Rat
Organism_taxid: 10116
Gene: Dlg4, Dlgh4, Psd95
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)

Molecule: Synthesized Gk Inhibitor
Chain: B
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: C 1 2 1
R_factor 0.222 R_Free 0.264
crystal
cell
length a length b length c angle alpha angle beta angle gamma
119.028 45.743 86.358 90.00 103.22 90.00
method X-Ray Diffractionresolution 2.35 Å
Primary referenceSynaptic Targeting and Function of SAPAPs Mediated by Phosphorylation-Dependent Binding to PSD-95 MAGUKs., Zhu J, Zhou Q, Shang Y, Li H, Peng M, Ke X, Weng Z, Zhang R, Huang X, Li SSC, Feng G, Lu Y, Zhang M, Cell Rep. 2017 Dec 26;21(13):3781-3793. doi: 10.1016/j.celrep.2017.11.107. PMID:29281827
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (51 Kb) [Save to disk]
  • Biological Unit Coordinates (5ypr.pdb1.gz) 46 Kb
  • CSU: Contacts of Structural Units for 5YPR
  • Structure Factors (403 Kb)
  • Retrieve 5YPR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5YPR from S2C, [Save to disk]
  • View 5YPR 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 5YPR
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ypr_B] [5ypr_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5YPR
  • Community annotation for 5YPR at PDBWiki (http://pdbwiki.org)

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