3EE6 Hydrolase date Sep 04, 2008
title Crystal Structure Analysis Of Tripeptidyl Peptidase -I
authors A.Pal, R.Kraetzner, M.Grapp, T.Gruene, K.Schreiber, M.Granborg, H. A.R.Asif, S.Becker, J.Gartner, G.M.Sheldrick, R.Steinfeld
compound source
Molecule: Tripeptidyl-Peptidase 1
Chain: A, B
Synonym: Tpp-1, Tripeptidyl-Peptidase I, Tpp-I, Tripeptidyl Aminopeptidase, Lysosomal Pepstatin-Insensitive Protease, L Growth-Inhibiting Gene 1 Protein;
Ec: 3.4.14.9
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cln2
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_strain: Hek 293 Cell Line
Expression_system_vector_type: Plamid
symmetry Space Group: P 21 21 2
R_factor 0.218 R_Free 0.262
crystal
cell
length a length b length c angle alpha angle beta angle gamma
113.450 128.930 100.500 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.35 Å
ligand CA, CL, NAG, SO4, ZN enzyme Hydrolase E.C.3.4.14.9 BRENDA
Primary referenceStructure of tripeptidyl-peptidase I provides insight into the molecular basis of late infantile neuronal ceroid lipofuscinosis., Pal A, Kraetzner R, Gruene T, Grapp M, Schreiber K, Gronborg M, Urlaub H, Becker S, Asif AR, Gartner J, Sheldrick GM, Steinfeld R, J Biol Chem. 2009 Feb 6;284(6):3976-84. Epub 2008 Nov 26. PMID:19038966
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (177 Kb) [Save to disk]
  • Biological Unit Coordinates (3ee6.pdb1.gz) 168 Kb
  • Biological Unit Coordinates (3ee6.pdb2.gz) 332 Kb
  • LPC: Ligand-Protein Contacts for 3EE6
  • CSU: Contacts of Structural Units for 3EE6
  • Likely Quarternary Molecular Structure file(s) for 3EE6
  • Structure Factors (969 Kb)
  • Retrieve 3EE6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3EE6 from S2C, [Save to disk]
  • Re-refined 3ee6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3EE6 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 3EE6
  • 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 3EE6, from MSDmotif at EBI
  • Fold representative 3ee6 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ee6] [3ee6_B] [3ee6_A]
  • SWISS-PROT database: [O14773]
  • Domain organization of [TPP1_HUMAN] by SWISSPFAM
  • Domain found in 3EE6: [Pro-kuma_activ ] by SMART
  • Alignments of the sequence of 3EE6 with the sequences similar proteins can be viewed for 3EE6's classification [TPP1_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [TPP1_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3EE6
  • Community annotation for 3EE6 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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