3JPY Transport Protein date Sep 04, 2009
title Crystal Structure Of The Zinc-Bound Amino Terminal Domain Of Receptor Subunit Nr2b
authors E.Karakas, N.Simorowski, H.Furukawa
compound source
Molecule: Glutamate [Nmda] Receptor Subunit Epsilon-2
Chain: A
Fragment: Amino Terminal Domain
Synonym: N-Methyl D-Aspartate Receptor Subtype 2b, Nmdar2b,
Engineered: Yes
Mutation: Yes
 Organism_scientific: Rattus Norvegicus
Organism_common: Brown Rat,Rat,Rats
Organism_taxid: 10116
Gene: Grin2b
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111
symmetry Space Group: P 31 2 1
R_factor 0.204 R_Free 0.233
crystal
cell
length a length b length c angle alpha angle beta angle gamma
143.368 143.368 88.467 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.21 Å
ligand CL, NA, NAG, ZN enzyme
Primary referenceStructure of the zinc-bound amino-terminal domain of the NMDA receptor NR2B subunit., Karakas E, Simorowski N, Furukawa H, EMBO J. 2009 Nov 12. PMID:19910922
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (60 Kb) [Save to disk]
  • Biological Unit Coordinates (3jpy.pdb1.gz) 54 Kb
  • Biological Unit Coordinates (3jpy.pdb2.gz) 107 Kb
  • LPC: Ligand-Protein Contacts for 3JPY
  • CSU: Contacts of Structural Units for 3JPY
  • Structure Factors (232 Kb)
  • Retrieve 3JPY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3JPY from S2C, [Save to disk]
  • Re-refined 3jpy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3JPY 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 3JPY
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3JPY, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3jpy_A] [3jpy]
  • SWISS-PROT database: [Q00960]
  • Belongs to the glutamate-gated ion channel (gic) family of neurotransmitter receptors according to TCDB.
  • Domain organization of [NMDE2_RAT] by SWISSPFAM
    • Other resources with information on 3JPY
  • Community annotation for 3JPY 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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