4D5M Hormone date Nov 05, 2014
title Gonadotropin-Releasing Hormone Agonist
authors P.Legrand, M.H.Le Du, C.Valery, S.Deville-Foillard, M.Paternost F.Artzner
compound source
Molecule: Triptorelin
Chain: A, B, C, D
Engineered: Yes
Other_details: Triptorelin Is A Medicine Available In A Num Countries Worldwide. It Is An Analogous Of The Gonadotropin Hormone. 5-Oxo-D-Prolyl-L-Histidyl-L-Tryptophanyl-L-Seryl-L D-Tryptophanyl-L-Leucyl-L-Arginyl-L-Prolyl-L-Glycinamide.
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Triptorelin Is A Medicine Available In A Num Countries Worldwide.
symmetry Space Group: C 1 2 1
R_factor 0.080 R_Free 0.087
crystal
cell
length a length b length c angle alpha angle beta angle gamma
84.900 27.470 13.150 90.00 98.83 90.00
method X-Ray Diffractionresolution 0.85 Å
ligand DTR, NH2, PCA, PO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceAtomic view of the histidine environment stabilizing higher-pH conformations of pH-dependent proteins., Valery C, Deville-Foillard S, Lefebvre C, Taberner N, Legrand P, Meneau F, Meriadec C, Delvaux C, Bizien T, Kasotakis E, Lopez-Iglesias C, Gall A, Bressanelli S, Le Du MH, Paternostre M, Artzner F, Nat Commun. 2015 Jul 20;6:7771. doi: 10.1038/ncomms8771. PMID:26190377
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (39 Kb) [Save to disk]
  • Biological Unit Coordinates (4d5m.pdb1.gz) 11 Kb
  • Biological Unit Coordinates (4d5m.pdb2.gz) 10 Kb
  • Biological Unit Coordinates (4d5m.pdb3.gz) 8 Kb
  • Biological Unit Coordinates (4d5m.pdb4.gz) 8 Kb
  • LPC: Ligand-Protein Contacts for 4D5M
  • CSU: Contacts of Structural Units for 4D5M
  • Structure Factors (484 Kb)
  • Retrieve 4D5M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4D5M from S2C, [Save to disk]
  • Re-refined 4d5m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4D5M 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 4D5M
  • 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 4d5m from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4d5m_D] [4d5m_A] [4d5m_C] [4d5m] [4d5m_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4D5M
  • Community annotation for 4D5M at PDBWiki (http://pdbwiki.org)

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