1K3B Hydrolase date Oct 02, 2001
title Crystal Structure Of Human Dipeptidyl Peptidase I (Cathepsin Exclusion Domain Added To An Endopeptidase Framework Create Machine For Activation Of Granular Serine Proteases
authors D.Turk, V.Janjic, I.Stern, M.Podobnik, D.Lamba, S.W.Dahl, C.Laurit J.Pedersen, V.Turk, B.Turk
compound source
Molecule: Dipeptydil-Peptidase I Exclusion Domain
Chain: A
Synonym: Dppi, Cathepsin C, Residual Propart
Ec: 3.4.14.1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_cell_line: High Five
Expression_system_cell: Insect Cell(Invitrogen)
Expression_system_vector_type: Baculovirus
Expression_system_vector: Pvl1393

Molecule: Dipeptydil-Peptidase I Light Chain
Chain: B
Synonym: Dppi, Cathepsin C, Beta Chain
Ec: 3.4.14.1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_cell_line: High Five
Expression_system_cell: Insect Cell(Invitrogen)
Expression_system_vector_type: Baculovirus
Expression_system_vector: Pvl1393

Molecule: Dipeptydil-Peptidase I Heavy Chain
Chain: C
Synonym: Dppi, Cathepsin C, Alpha Chain
Ec: 3.4.14.1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_cell_line: High Five
Expression_system_cell: Insect Cell(Invitrogen)
Expression_system_vector_type: Baculovirus
Expression_system_vector: Pvl1393
symmetry Space Group: I 2 2 2
R_factor 0.190 R_Free 0.231
crystal
cell
length a length b length c angle alpha angle beta angle gamma
87.154 88.031 114.609 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.15 Å
ligand CL, NAG, SO4 enzyme Hydrolase E.C.3.4.14.1 BRENDA
related structures by homologous chain: 1BP4, 1JQP, 1POP
Gene
Ontology
ChainFunctionProcessComponent
C, B


Primary referenceStructure of human dipeptidyl peptidase I (cathepsin C): exclusion domain added to an endopeptidase framework creates the machine for activation of granular serine proteases., Turk D, Janjic V, Stern I, Podobnik M, Lamba D, Dahl SW, Lauritzen C, Pedersen J, Turk V, Turk B, EMBO J 2001 Dec 3;20(23):6570-82. PMID:11726493
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (73 Kb) [Save to disk]
  • Biological Unit Coordinates (1k3b.pdb1.gz) 263 Kb
  • LPC: Ligand-Protein Contacts for 1K3B
  • CSU: Contacts of Structural Units for 1K3B
  • Likely Quarternary Molecular Structure file(s) for 1K3B
  • Structure Factors (187 Kb)
  • Retrieve 1K3B in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1K3B from S2C, [Save to disk]
  • Re-refined 1k3b structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1K3B 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 1K3B
  • 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 1K3B, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1k3ba_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1k3b.1, region B:,C [Jmol] [rasmolscript] [script source]
  • Fold representative 1k3b from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1k3b_C] [1k3b_B] [1k3b_A] [1k3b]
  • SWISS-PROT database: [P53634]
  • Domain organization of [CATC_HUMAN] by SWISSPFAM
  • Domain found in 1K3B: [Pept_C1 ] by SMART
  • Other resources with information on 1K3B
  • Community annotation for 1K3B at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science