4URT Protein Binding date Jul 02, 2014
title The Crystal Structure Of A Fragment Of Netrin-1 In Complex W Fn6 Of Dcc
authors L.I.Finci, N.Krueger, X.Sun, J.Zhang, M.Chegkazi, Y.Wu, G.Schenk, H.D.T.Mertens, D.I.Svergun, Y.Zhang, J.H.Wang, R.Meijers
compound source
Molecule: Netrin-1
Chain: A
Fragment: Vi And V Domains, Residues 39-453
Synonym: Epididymis Tissue Protein Li 131p
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Netrin Receptor Dcc
Chain: B
Fragment: Fn5-Fn6, Residues 844-1043
Synonym: Colorectal Cancer Suppressor, Immunoglobulin Super Subclass Member 1, Tumor Suppressor Protein Dcc, Deleted In Colorectal Cancer

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 21 21 21
R_factor 0.230 R_Free 0.265
length a length b length c angle alpha angle beta angle gamma
84.650 87.410 155.317 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.10 Å
ligand CA, CL, GOL, NAG, SO4 enzyme

Primary referenceThe Crystal Structure of Netrin-1 in Complex with DCC Reveals the Bifunctionality of Netrin-1 As a Guidance Cue., Finci LI, Kruger N, Sun X, Zhang J, Chegkazi M, Wu Y, Schenk G, Mertens HD, Svergun DI, Zhang Y, Wang JH, Meijers R, Neuron. 2014 Aug 20;83(4):839-49. doi: 10.1016/j.neuron.2014.07.010. Epub 2014, Aug 7. PMID:25123307
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (108 Kb) [Save to disk]
  • Biological Unit Coordinates (4urt.pdb1.gz) 133 Kb
  • LPC: Ligand-Protein Contacts for 4URT
  • CSU: Contacts of Structural Units for 4URT
  • Structure Factors (164 Kb)
  • Retrieve 4URT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4URT from S2C, [Save to disk]
  • Re-refined 4urt structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4URT 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 4URT
  • 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 4URT, from MSDmotif at EBI
  • Fold representative 4urt from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4urt_B] [4urt_A] [4urt]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4URT: [EGF_Lam] [FN3] [LamNT ] by SMART
  • Other resources with information on 4URT
  • Community annotation for 4URT at PDBWiki (http://pdbwiki.org)

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