5V5W Cell Adhesion date Mar 15, 2017
title Molecular Mechanism Of Mdga1: Regulation Of Neuroligin 2:Neu Trans-Synaptic Bridges
authors M.Machius, S.P.Gangwar, G.Rudenko
compound source
Molecule: Mam Domain-Containing Glycosylphosphatidylinosito Protein 1;
Chain: A
Synonym: Gpi And Mam Protein,Gpim,Glycosylphosphatidylinosi Mam Domain-Containing Protein 3;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mdga1, Mamdc3
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111
Expression_system_cell_line: High Five
Expression_system_vector_type: Baculovirus
Expression_system_vector: Pfastbac1-Hm
symmetry Space Group: I 2 3
R_factor 0.214 R_Free 0.256
crystal
cell
length a length b length c angle alpha angle beta angle gamma
139.068 139.068 139.068 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.72 Å
ligand SO4 enzyme
Primary referenceMolecular Mechanism of MDGA1: Regulation of Neuroligin 2:Neurexin Trans-synaptic Bridges., Gangwar SP, Zhong X, Seshadrinathan S, Chen H, Machius M, Rudenko G, Neuron. 2017 Jun 21;94(6):1132-1141.e4. doi: 10.1016/j.neuron.2017.06.009. PMID:28641112
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (104 Kb) [Save to disk]
  • Biological Unit Coordinates (5v5w.pdb1.gz) 98 Kb
  • Biological Unit Coordinates (5v5w.pdb2.gz) 291 Kb
  • LPC: Ligand-Protein Contacts for 5V5W
  • CSU: Contacts of Structural Units for 5V5W
  • Structure Factors (339 Kb)
  • Retrieve 5V5W in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5V5W from S2C, [Save to disk]
  • Re-refined 5v5w structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5V5W 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 5V5W
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5v5w_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5V5W
  • Community annotation for 5V5W at PDBWiki (http://pdbwiki.org)

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