3ZYI Cell Adhesion date Aug 23, 2011
title Netring2 In Complex With Ngl2
authors E.Seiradake, C.H.Coles, P.V.Perestenko, K.Harlos, R.A.J.Mcilhinn A.R.Aricescu, E.Y.Jones
compound source
Molecule: Leucine-Rich Repeat-Containing Protein 4
Chain: A
Fragment: Lrr And Ig Domains, Residues 1-444
Synonym: Brain Tumor-Associated Protein Bag, Nasopharyngeal Carcinoma-Associated Gene 14 Protein, Netrin-G2 Ligand, Ngl
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hek 293 Gnti(-)
Expression_system_plasmid: Phlsec

Molecule: Netrin-G2
Chain: B
Fragment: Lam And Egf1 Domains, Residues 423-767
Synonym: Laminet-2, Netring2
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: 293 Hek Gnti (-)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Phlsec
symmetry Space Group: I 2 2 2
R_factor 0.243 R_Free 0.287
crystal
cell
length a length b length c angle alpha angle beta angle gamma
75.420 153.390 158.730 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand CA, NAG, PO4 enzyme
Primary referenceStructural basis for cell surface patterning through NetrinG-NGL interactions., Seiradake E, Coles CH, Perestenko PV, Harlos K, McIlhinney RA, Aricescu AR, Jones EY, EMBO J. 2011 Sep 23. doi: 10.1038/emboj.2011.346. PMID:21946559
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (115 Kb) [Save to disk]
  • Biological Unit Coordinates (3zyi.pdb1.gz) 109 Kb
  • LPC: Ligand-Protein Contacts for 3ZYI
  • CSU: Contacts of Structural Units for 3ZYI
  • Structure Factors (556 Kb)
  • Retrieve 3ZYI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3ZYI from S2C, [Save to disk]
  • Re-refined 3zyi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3ZYI 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 3ZYI
  • 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 3ZYI, from MSDmotif at EBI
  • Fold representative 3zyi from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3zyi_A] [3zyi] [3zyi_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3ZYI: [EGF_Lam] [IGc2] [LRR] [LRRCT] [LRRNT] [LRR_TYP] [LamNT ] by SMART
  • Other resources with information on 3ZYI
  • Community annotation for 3ZYI at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science