1PBQ Ligand Binding Protein date May 14, 2003
title Crystal Structure Of The Nr1 Ligand Binding Core In Complex Dichlorokynurenic Acid (Dcka) At 1.90 Angstroms Resolution
authors H.Furukawa, E.Gouaux
compound source
Molecule: N-Methyl-D-Aspartate Receptor Subunit 1
Chain: A, B
Fragment: Ligand Binding Core
Engineered: Yes
Organism_scientific: Rattus Norvegicus
Organism_common: Norway Rat
Organism_taxid: 10116
Organ: Forebrain
Gene: Grin1 Or Nmdar1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Origamib (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b(+)
symmetry Space Group: C 1 2 1
R_factor 0.231 R_Free 0.270
crystal
cell
length a length b length c angle alpha angle beta angle gamma
85.700 65.300 124.300 90.00 98.10 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand DK1 BindingDB enzyme
related structures by homologous chain: 1PB9
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceMechanisms of activation, inhibition and specificity: crystal structures of the NMDA receptor NR1 ligand-binding core., Furukawa H, Gouaux E, EMBO J 2003 Jun 16;22(12):2873-85. PMID:12805203
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (99 Kb) [Save to disk]
  • Biological Unit Coordinates (1pbq.pdb1.gz) 49 Kb
  • Biological Unit Coordinates (1pbq.pdb2.gz) 48 Kb
  • LPC: Ligand-Protein Contacts for 1PBQ
  • CSU: Contacts of Structural Units for 1PBQ
  • Likely Quarternary Molecular Structure file(s) for 1PBQ
  • Retrieve 1PBQ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1PBQ from S2C, [Save to disk]
  • View 1PBQ 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 1PBQ
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1PBQ, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1pbqa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1pbqb_, region B [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1pbq_B] [1pbq_A] [1pbq]
  • SWISS-PROT database: [P35439]
  • Belongs to the glutamate-gated ion channel (gic) family of neurotransmitter receptors according to TCDB.
  • Domain organization of [NMDZ1_RAT] by SWISSPFAM
  • Domains found in 1PBQ: [Lig_chan-Glu_bd] [PBPb] [PBPe ] by SMART
  • Other resources with information on 1PBQ
  • Community annotation for 1PBQ 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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