3EDY Hydrolase date Sep 03, 2008
title Crystal Structure Of The Precursor Form Of Human Tripeptidyl
authors J.Guhaniyogi, I.Sohar, K.Das, P.Lobel, A.M.Stock
compound source
Molecule: Tripeptidyl-Peptidase 1
Chain: A
Fragment: Residues 20-563
Synonym: Tripeptidyl-Peptidase I, Tpp-1, Tpp-I, Tripeptidyl Aminopeptidase, Lysosomal Pepstatin- Insensitive Protease, Growth-Inhibiting Gene 1 Protein;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tpp1, Cln2
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
Expression_system_cell: Ovary Cells
symmetry Space Group: P 21 21 21
R_factor 0.179 R_Free 0.205
length a length b length c angle alpha angle beta angle gamma
59.807 93.173 102.479 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.85 Å
ligand CA, EDO, NAG enzyme Hydrolase E.C. BRENDA

Primary referenceCrystal Structure and Autoactivation Pathway of the Precursor Form of Human Tripeptidyl-peptidase 1, the Enzyme Deficient in Late Infantile Ceroid Lipofuscinosis., Guhaniyogi J, Sohar I, Das K, Stock AM, Lobel P, J Biol Chem. 2009 Feb 6;284(6):3985-97. Epub 2008 Nov 26. PMID:19038967
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (98 Kb) [Save to disk]
  • Biological Unit Coordinates (3edy.pdb1.gz) 92 Kb
  • LPC: Ligand-Protein Contacts for 3EDY
  • CSU: Contacts of Structural Units for 3EDY
  • Likely Quarternary Molecular Structure file(s) for 3EDY
  • Structure Factors (355 Kb)
  • Retrieve 3EDY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3EDY from S2C, [Save to disk]
  • Re-refined 3edy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3EDY 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 3EDY
  • 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 3EDY, from MSDmotif at EBI
  • Fold representative 3edy from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3edy] [3edy_A]
  • SWISS-PROT database: [O14773]
  • Domain organization of [TPP1_HUMAN] by SWISSPFAM
  • Domain found in 3EDY: [Pro-kuma_activ ] by SMART
  • Other resources with information on 3EDY
  • Community annotation for 3EDY 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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