5YPO Protein Binding date Nov 02, 2017
title Crystal Structure Of Psd-95 Gk Domain In Complex With Phosph Peptide
authors J.Zhu, Q.Zhou, Y.Shang, Z.Weng, R.Zhang, M.Zhang
compound source
Molecule: Disks Large Homolog 4
Chain: B, 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: Sapap
Chain: C, D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: P 21 21 21
R_factor 0.179 R_Free 0.226
crystal
cell
length a length b length c angle alpha angle beta angle gamma
33.776 84.063 165.123 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.29 Å
ligand GOL, SEP enzyme
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] (73 Kb) [Save to disk]
  • Biological Unit Coordinates (5ypo.pdb1.gz) 36 Kb
  • Biological Unit Coordinates (5ypo.pdb2.gz) 35 Kb
  • LPC: Ligand-Protein Contacts for 5YPO
  • CSU: Contacts of Structural Units for 5YPO
  • Structure Factors (519 Kb)
  • Retrieve 5YPO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5YPO from S2C, [Save to disk]
  • View 5YPO 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 5YPO
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5ypo from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ypo_D] [5ypo_B] [5ypo_A] [5ypo_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5YPO
  • Community annotation for 5YPO at PDBWiki (http://pdbwiki.org)

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