6YPE Cell Adhesion date Apr 15, 2020
title Crystal Structure Of The Human Neuronal Pentraxin 1 (Np1) Pe (Ptx) Domain.
authors J.Elegheert, A.J.Clayton, A.R.Aricescu
compound source
Molecule: Neuronal Pentraxin-1
Chain: A, B
Synonym: Np1,Neuronal Pentraxin I,Np-I
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nptx1
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293t
Expression_system_atcc_number: Crl-1573
Expression_system_plasmid: Phlsec
symmetry Space Group: C 1 2 1
R_factor 0.153 R_Free 0.178
length a length b length c angle alpha angle beta angle gamma
121.220 36.060 92.170 90.00 97.47 90.00
method X-Ray Diffractionresolution 1.45 Å
ligand CA, CAC enzyme
Primary referenceA synthetic synaptic organizer protein restores glutamatergic neuronal circuits., Suzuki K, Elegheert J, Song I, Sasakura H, Senkov O, Matsuda K, Kakegawa W, Clayton AJ, Chang VT, Ferrer-Ferrer M, Miura E, Kaushik R, Ikeno M, Morioka Y, Takeuchi Y, Shimada T, Otsuka S, Stoyanov S, Watanabe M, Takeuchi K, Dityatev A, Aricescu AR, Yuzaki M, Science. 2020 Aug 28;369(6507). pii: 369/6507/eabb4853. doi:, 10.1126/science.abb4853. PMID:32855309
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (149 Kb) [Save to disk]
  • Biological Unit Coordinates (6ype.pdb1.gz) 71 Kb
  • Biological Unit Coordinates (6ype.pdb2.gz) 69 Kb
  • LPC: Ligand-Protein Contacts for 6YPE
  • CSU: Contacts of Structural Units for 6YPE
  • Structure Factors (2220 Kb)
  • Retrieve 6YPE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6YPE from S2C, [Save to disk]
  • View 6YPE 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 6YPE
  • 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 6ype from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6ype_A] [6ype_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6YPE
  • Community annotation for 6YPE at PDBWiki (http://pdbwiki.org)

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