3TBD Cell Adhesion date Aug 05, 2011
title Crystal Structure Of Domain Vi And Le1 Of Human Netrin-G2
authors J.Brasch, Q.Liu, L.Shapiro
compound source
Molecule: Netrin-G2
Chain: A
Fragment: Domain Vi And Le1, Unp Residues 18-349
Synonym: Laminet-2
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ntng2, Kiaa1857, Lmnt2, Unq9381pro34206
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
Expression_system_cell_line: Hek 293 Gnti(-)
Expression_system_vector_type: Episomal
Expression_system_plasmid: Pcep4
symmetry Space Group: P 32 2 1
R_factor 0.175 R_Free 0.227
length a length b length c angle alpha angle beta angle gamma
63.134 63.134 190.640 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.80 Å
ligand CA, CL, NAG, PO4 enzyme
Primary referenceCrystal structure of the ligand binding domain of netrin g2., Brasch J, Harrison OJ, Ahlsen G, Liu Q, Shapiro L, J Mol Biol. 2011 Dec 16;414(5):723-34. Epub 2011 Oct 25. PMID:22041449
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (74 Kb) [Save to disk]
  • Biological Unit Coordinates (3tbd.pdb1.gz) 67 Kb
  • LPC: Ligand-Protein Contacts for 3TBD
  • CSU: Contacts of Structural Units for 3TBD
  • Structure Factors (670 Kb)
  • Retrieve 3TBD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3TBD from S2C, [Save to disk]
  • Re-refined 3tbd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3TBD 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 3TBD
  • 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
  • 3D motif for 3TBD, from MSDmotif at EBI
  • Fold representative 3tbd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3tbd] [3tbd_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3TBD: [EGF_Lam] [LamNT ] by SMART
  • Other resources with information on 3TBD
  • Community annotation for 3TBD at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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