1BP4 Hydrolase date Aug 12, 1998
title Use Of Papain As A Model For The Structure-Based Design Of C Inhibitors. Crystal Structures Of Two Papain Inhibitor Comp Demonstrate Binding To S'-Subsites.
authors J.M.Lalonde, B.Zhao, W.W.Smith, C.A.Janson, R.L.Desjarlais, T.A.T T.J.Carr, S.K.Thompson, D.S.Yamashita, D.F.Veber, S.S.Abdel-Meq
compound source
Molecule: Papain
Chain: A
Fragment: Non
Other_details: Aldehyde Inhibitor Covalently Bound To Activ 25 As A Hemimercaptal. Bond Occurs Between Cys 25-Sg And Al
Organism_scientific: Carica Papaya
Organism_common: Papaya
Organism_taxid: 3649
symmetry Space Group: C 1 2 1
R_factor 0.190 R_Free 0.240
crystal
cell
length a length b length c angle alpha angle beta angle gamma
100.540 50.740 62.280 90.00 99.90 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand ALD enzyme
related structures by homologous chain: 1K3B, 1STF
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceUse of papain as a model for the structure-based design of cathepsin K inhibitors: crystal structures of two papain-inhibitor complexes demonstrate binding to S'-subsites., LaLonde JM, Zhao B, Smith WW, Janson CA, DesJarlais RL, Tomaszek TA, Carr TJ, Thompson SK, Oh HJ, Yamashita DS, Veber DF, Abdel-Meguid SS, J Med Chem 1998 Nov 5;41(23):4567-76. PMID:9804696
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (41 Kb) [Save to disk]
  • Biological Unit Coordinates (1bp4.pdb1.gz) 37 Kb
  • LPC: Ligand-Protein Contacts for 1BP4
  • CSU: Contacts of Structural Units for 1BP4
  • Likely Quarternary Molecular Structure file(s) for 1BP4
  • Retrieve 1BP4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1BP4 from S2C, [Save to disk]
  • View 1BP4 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 1BP4
  • 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 1BP4, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1bp4__, region [Jmol] [rasmolscript] [script source]
  • Fold representative 1bp4 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: [1bp4] [1bp4_A]
  • SWISS-PROT database: [P00784]
  • Domain organization of [PAPA1_CARPA] by SWISSPFAM
  • Domain found in 1BP4: [Pept_C1 ] by SMART
  • Other resources with information on 1BP4
  • Community annotation for 1BP4 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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