6FKQ Signaling Protein date Jan 24, 2018
title The Crystal Structure Of A Fragment Of Netrin-1 In Complex W Fragment Of Draxin
authors T.Bhowmick, R.Meijers
compound source
Molecule: Netrin-1
Chain: A
Synonym: Epididymis Tissue Protein Li 131p
Engineered: Yes
Other_details: Netrin-1 Is A Prototypical Axon Guidance Cue Binds To The Receptor Deleted In Colorectal Cancer (Dcc).;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ntn1, Ntn1l
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293t
Expression_system_atcc_number: 293t17 [Hek 293t17] Atcc C
Expression_system_tissue: Kidney
Expression_system_plasmid: Pxlg

Molecule: Draxin
Chain: B
Fragment: Unp Residues 225-243
Synonym: Dorsal Inhibitory Axon Guidance Protein,Dorsal Rep Axon Guidance Protein,Neucrin;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Draxin, C1orf187, Psec0258, Unq3119pro10268
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293t
Expression_system_atcc_number: (Hek 293t17] Atcc Crl-11268
Expression_system_tissue: Kidney
Expression_system_plasmid: Pxlg
symmetry Space Group: P 64 2 2
R_factor 0.235 R_Free 0.271
crystal
cell
length a length b length c angle alpha angle beta angle gamma
130.794 130.794 183.870 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.07 Å
Gene
Ontology
ChainFunctionProcessComponent
B


Primary referenceStructural Basis for Draxin-Modulated Axon Guidance and Fasciculation by Netrin-1 through DCC., Liu Y, Bhowmick T, Liu Y, Gao X, Mertens HDT, Svergun DI, Xiao J, Zhang Y, Wang JH, Meijers R, Neuron. 2018 Feb 20. pii: S0896-6273(18)30109-0. doi:, 10.1016/j.neuron.2018.02.010. PMID:29503192
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (80 Kb) [Save to disk]
  • Biological Unit Coordinates (6fkq.pdb1.gz) 73 Kb
  • CSU: Contacts of Structural Units for 6FKQ
  • Structure Factors (373 Kb)
  • Retrieve 6FKQ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6FKQ from S2C, [Save to disk]
  • View 6FKQ 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 6FKQ
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 6fkq from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6fkq_B] [6fkq_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6FKQ
  • Community annotation for 6FKQ at PDBWiki (http://pdbwiki.org)

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