1Y1M	Ligand Binding Protein	date	Nov 18, 2004
title	Crystal Structure Of The Nr1 Ligand Binding Core In Complex Cycloleucine
authors	A.Inanobe, E.Gouaux
compound		source
Molecule: Glutamate [Nmda] Receptor Subunit Zeta 1 Chain: A, B Fragment: Ligand-Binding Core Synonym: Nmdar Nr1; Nr1; Nmd-R1; N-Methyl-D-Aspartate Recep Glutamate Receptor, Ionotropic, N-Methyl D-Aspartate 1; Engineered: Yes		Organism_scientific: Rattus Norvegicus Organism_common: Norway Rat Organism_taxid: 10116 Organ: Forebrain Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Origami B Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet22b(+) Other_details: The First Gly Is A Cloning Artifact. Two Reg (Residues 394: 544 And 631:800) Of Nmz1_rat Were Connected W Dipeptide Of Gly And Thr
symmetry	Space Group: P 1	R_factor 0.187 R_Free 0.224
crystal cell	length a length b length c angle alpha angle beta angle gamma 53.156 53.203 67.546 110.12 91.55 108.69
method	X-Ray Diffraction	resolution	1.80 Å
ligand	AC5	enzyme
Gene Ontology	Chain Function Process Component A, B
Primary reference	Mechanism of Partial Agonist Action at the NR1 Subunit of NMDA Receptors., Inanobe A, Furukawa H, Gouaux E, Neuron 2005 Jul 7;47(1):71-84. PMID:15996549

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (103 Kb) [Save to disk] Biological Unit Coordinates (1y1m.pdb1.gz) 51 Kb Biological Unit Coordinates (1y1m.pdb2.gz) 50 Kb Biological Unit Coordinates (1y1m.pdb3.gz) 98 Kb LPC: Ligand-Protein Contacts for 1Y1M CSU: Contacts of Structural Units for 1Y1M Likely Quarternary Molecular Structure file(s) for 1Y1M Structure Factors (481 Kb) Retrieve 1Y1M in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1Y1M from S2C, [Save to disk] Re-refined 1y1m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1Y1M 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 1Y1M

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 1Y1M, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1y1m_B] [1y1m] [1y1m_A] 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 1Y1M: [Lig_chan-Glu_bd] [PBPb] [PBPe ] by SMART

Other resources with information on 1Y1M

Community annotation for 1Y1M at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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