4N1D Cytokine, Signaling Protein date Oct 04, 2013
title Nodalbmp2 Chimera Nb250
authors L.Esquivies
compound source
Molecule: Nodalbmp2 Chimera Protein
Chain: A
Synonym: Bmp-2, Bone Morphogenetic Protein 2a, Bmp-2a
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Bmp2, Bmp2a, Nodal
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: H 3 2
R_factor 0.175 R_Free 0.204
length a length b length c angle alpha angle beta angle gamma
95.570 95.570 97.494 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.91 Å

Primary referenceDesigner Nodal/BMP2 Chimeras Mimic Nodal Signaling, Promote Chondrogenesis, and Reveal a BMP2-like Structure., Esquivies L, Blackler A, Peran M, Rodriguez-Esteban C, Izpisua Belmonte JC, Booker E, Gray PC, Ahn C, Kwiatkowski W, Choe S, J Biol Chem. 2014 Jan 17;289(3):1788-97. doi: 10.1074/jbc.M113.529180. Epub 2013 , Dec 5. PMID:24311780
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (44 Kb) [Save to disk]
  • Biological Unit Coordinates (4n1d.pdb1.gz) 75 Kb
  • CSU: Contacts of Structural Units for 4N1D
  • Structure Factors (611 Kb)
  • Retrieve 4N1D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4N1D from S2C, [Save to disk]
  • Re-refined 4n1d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4N1D 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 4N1D
  • 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 4N1D, from MSDmotif at EBI
  • Fold representative 4n1d from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4n1d] [4n1d_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4N1D: [TGFB ] by SMART
  • Other resources with information on 4N1D
  • Community annotation for 4N1D at PDBWiki (http://pdbwiki.org)

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