3ZYJ Cell Adhesion date Aug 23, 2011
title Netring1 In Complex With Ngl1
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 4c
Chain: A, C
Fragment: Lrr And Ig Domains, 44-444
Synonym: Ngl1, Netrin-G1 Ligand, Ngl-1
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_vector_type: Plasmid
Expression_system_plasmid: Phlsec

Molecule: Netrin-G1
Chain: B, D
Fragment: Lam And Egf1 Domains, 365-783
Synonym: Netring1, Laminet-1
Engineered: Yes
Mutation: 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_vector_type: Plasmid
Expression_system_plasmid: Phlsec
symmetry Space Group: F 2 2 2
R_factor 0.256 R_Free 0.268
crystal
cell
length a length b length c angle alpha angle beta angle gamma
184.420 204.430 288.070 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.25 Å
ligand BMA, CA, MAN, NAG 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] (478 Kb) [Save to disk]
  • Biological Unit Coordinates (3zyj.pdb1.gz) 237 Kb
  • Biological Unit Coordinates (3zyj.pdb2.gz) 237 Kb
  • LPC: Ligand-Protein Contacts for 3ZYJ
  • CSU: Contacts of Structural Units for 3ZYJ
  • Structure Factors (590 Kb)
  • Retrieve 3ZYJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3ZYJ from S2C, [Save to disk]
  • Re-refined 3zyj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3ZYJ 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 3ZYJ
  • 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 3ZYJ, from MSDmotif at EBI
  • Fold representative 3zyj from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3zyj] [3zyj_A] [3zyj_B] [3zyj_C] [3zyj_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3ZYJ: [EGF_Lam] [EGF_like] [IGc2] [LRR] [LRRCT] [LRRNT] [LRR_TYP] [LamNT ] by SMART
  • Other resources with information on 3ZYJ
  • Community annotation for 3ZYJ at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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