5EWM Transport Protein date Nov 20, 2015
title Crystal Structure Of Amino Terminal Domains Of The Nmda Rece Subunit Glun1 And Glun2b In Complex With Evt-101
authors J.Pandit
compound source
Molecule: Nmda Glutamate Receptor Subunit
Chain: A, C
Fragment: Amino Terminal Domain (Unp Residues 23-408)
Engineered: Yes
Mutation: Yes
Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Gene: Grin1, Nr1
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_vector_type: Baculovirus

Molecule: Glutamate Receptor Ionotropic, Nmda 2b
Chain: B, D
Fragment: Amino Terminal Domain (Unp Residues 31-394)
Synonym: Glun2b,Glutamate [Nmda] Receptor Subunit Epsilon-2 D-Aspartate Receptor Subtype 2b,Nr2b,N-Methyl-D-Aspartate R Subunit 3,Hnr3;
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Grin2b, Nmdar2b
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_vector_type: Baculovirus
symmetry Space Group: C 1 2 1
R_factor 0.171 R_Free 0.211
crystal
cell
length a length b length c angle alpha angle beta angle gamma
268.400 60.610 144.500 90.00 116.27 90.00
method X-Ray Diffractionresolution 2.76 Å
ligand 5SM, BMA, MAN, NA, NAG enzyme
Primary referenceA novel binding mode reveals two distinct classes of NMDA receptor GluN2B-selective antagonists., Stroebel D, Buhl DL, Knafels JD, Chanda PK, Green M, Sciabola S, Mony L, Paoletti P, Pandit J, Mol Pharmacol. 2016 Feb 24. pii: mol.115.103036. PMID:26912815
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (479 Kb) [Save to disk]
  • Biological Unit Coordinates (5ewm.pdb1.gz) 239 Kb
  • Biological Unit Coordinates (5ewm.pdb2.gz) 236 Kb
  • LPC: Ligand-Protein Contacts for 5EWM
  • CSU: Contacts of Structural Units for 5EWM
  • Structure Factors (1469 Kb)
  • Retrieve 5EWM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5EWM from S2C, [Save to disk]
  • Re-refined 5ewm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5EWM 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 5EWM
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5ewm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ewm_B] [5ewm_A] [5ewm] [5ewm_C] [5ewm_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5EWM
  • Community annotation for 5EWM at PDBWiki (http://pdbwiki.org)

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