1QDQ Hydrolase date Jul 10, 1999
title X-Ray Crystal Structure Of Bovine Cathepsin B-Ca074 Complex
authors A.Yamamoto
compound source
Molecule: Cathepsin B
Chain: A
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
symmetry Space Group: P 43 21 2
R_factor 0.152 R_Free 0.183
length a length b length c angle alpha angle beta angle gamma
73.060 73.060 141.790 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.18 Å
ligand 074 BindingDB enzyme Hydrolase E.C. BRENDA
related structures by homologous chain: 1CSB, 1SP4

Primary referenceSubstrate specificity of bovine cathepsin B and its inhibition by CA074, based on crystal structure refinement of the complex., Yamamoto A, Tomoo K, Hara T, Murata M, Kitamura K, Ishida T, J Biochem (Tokyo) 2000 Apr;127(4):635-43. PMID:10739956
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (47 Kb) [Save to disk]
  • Biological Unit Coordinates (1qdq.pdb1.gz) 43 Kb
  • LPC: Ligand-Protein Contacts for 1QDQ
  • CSU: Contacts of Structural Units for 1QDQ
  • Likely Quarternary Molecular Structure file(s) for 1QDQ
  • Structure Factors (144 Kb)
  • Retrieve 1QDQ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1QDQ from S2C, [Save to disk]
  • Re-refined 1qdq structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1QDQ 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 1QDQ
  • 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 1QDQ, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1qdqa_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1qdq 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: [1qdq_A] [1qdq]
  • SWISS-PROT database: [P07688]
  • Domain organization of [CATB_BOVIN] by SWISSPFAM
  • Domain found in 1QDQ: [Pept_C1 ] by SMART
  • Other resources with information on 1QDQ
  • Community annotation for 1QDQ 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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