1PBH Thiol Protease date Feb 14, 1997
title Crystal Structure Of Human Recombinant Procathepsin B At 3.2 Angstrom Resolution
authors M.Podobnik, D.Turk
compound source
Molecule: Procathepsin B
Chain: A
Ec: 3.4.22.1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Bl21
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 (De3) Plyss
Expression_system_vector_type: Plasmid
Expression_system_vector: Pet3a
Expression_system_plasmid: Bl21
symmetry Space Group: P 21 21 21
R_factor 0.216 R_Free 0.252
crystal
cell
length a length b length c angle alpha angle beta angle gamma
44.950 77.100 97.330 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.20 Å
ligand
enzyme Hydrolase E.C.3.4.22.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structures of human procathepsin B at 3.2 and 3.3 Angstroms resolution reveal an interaction motif between a papain-like cysteine protease and its propeptide., Turk D, Podobnik M, Kuhelj R, Dolinar M, Turk V, FEBS Lett 1996 Apr 22;384(3):211-4. PMID:8617355
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (56 Kb) [Save to disk]
  • Biological Unit Coordinates (1pbh.pdb1.gz) 52 Kb
  • CSU: Contacts of Structural Units for 1PBH
  • Likely Quarternary Molecular Structure file(s) for 1PBH
  • Retrieve 1PBH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1PBH from S2C, [Save to disk]
  • View 1PBH 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 1PBH
  • 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
  • 3D motif for 1PBH, from MSDmotif at EBI
  • Genome occurence of 1PBH's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1pbh__, region [Jmol] [rasmolscript] [script source]
  • Fold representative 1pbh 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: [1pbh_A] [1pbh]
  • SWISS-PROT database: [P07858]
  • Domain organization of [CATB_HUMAN] by SWISSPFAM
  • Domain found in 1PBH: [Pept_C1 ] by SMART
  • Other resources with information on 1PBH
  • Community annotation for 1PBH at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Domain movements in 1PBH from the Database of Macromolecular Movements.
  • Images from IMB Jena Image Library of Biological Macromolecules.

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