2IFG Transferase date Sep 20, 2006
title Structure Of The Extracellular Segment Of Human Trka In Comp Nerve Growth Factor
authors X.He, K.C.Garcia
compound source
Molecule: High Affinity Nerve Growth Factor Receptor
Chain: A, B
Synonym: Neurotrophic Tyrosine Kinase Receptor Type 1, Trk1 Transforming Tyrosine Kinase Protein, P140-Trka, Trk-A;
Ec: 2.7.10.1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ntrk1, Trk
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_strain: Tn5
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pacgp67a

Molecule: Beta-Nerve Growth Factor
Chain: E, F
Synonym: Beta-Ngf
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ngfb
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
symmetry Space Group: P 1 21 1
R_factor 0.297 R_Free 0.331
crystal
cell
length a length b length c angle alpha angle beta angle gamma
110.215 81.681 115.748 90.00 104.15 90.00
method X-Ray Diffractionresolution 3.40 Å
ligand BMA, MAN, NAG, NDG enzyme Transferase E.C.2.7.10.1 BRENDA
Primary referenceStructural and mechanistic insights into nerve growth factor interactions with the TrkA and p75 receptors., Wehrman T, He X, Raab B, Dukipatti A, Blau H, Garcia KC, Neuron. 2007 Jan 4;53(1):25-38. PMID:17196528
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (157 Kb) [Save to disk]
  • Biological Unit Coordinates (2ifg.pdb1.gz) 148 Kb
  • LPC: Ligand-Protein Contacts for 2IFG
  • CSU: Contacts of Structural Units for 2IFG
  • Likely Quarternary Molecular Structure file(s) for 2IFG
  • Structure Factors (232 Kb)
  • Retrieve 2IFG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2IFG from S2C, [Save to disk]
  • Re-refined 2ifg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2IFG 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 2IFG
  • 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 2IFG, from MSDmotif at EBI
  • Fold representative 2ifg from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ifg_A] [2ifg_F] [2ifg_E] [2ifg_B] [2ifg]
  • SWISS-PROT database: [P01138] [P04629]
  • Domain organization of [NGF_HUMAN] [NTRK1_HUMAN] by SWISSPFAM
  • Domains found in 2IFG: [IG] [LRRCT] [NGF ] by SMART
  • Other resources with information on 2IFG
  • Community annotation for 2IFG at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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