1GMY Hydrolase Inhibitor date Sep 25, 2001
title Cathepsin B Complexed With Dipeptidyl Nitrile Inhibitor
authors P.D.Greenspan, K.L.Clark, R.A.Tommasi, S.D.Cowen, L.W.Mcquire, D. J.H.Van Duzer, R.L.Goldberg, H.Zhou, Z.Du, J.J.Fitt, D.E.Coppa, Z W.Macchia, L.Zhu, M.P.Capparelli, R.Goldstein, A.M.Wigg, J.R.Dou R.S.Bohacek, A.K.Knap
compound source
Molecule: Cathepsin B
Chain: A, B, C
Fragment: Protease Domain, Residues 80-333
Ec: 3.4.22.1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_vector_type: Baculovirus
symmetry Space Group: P 32 2 1
R_factor 0.161 R_Free 0.199
crystal
cell
length a length b length c angle alpha angle beta angle gamma
103.900 103.900 125.600 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.90 Å
ligand AEM, APD, DFA enzyme Hydrolase E.C.3.4.22.1 BRENDA
related structures by homologous chain: 1THE
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


Primary referenceIdentification of dipeptidyl nitriles as potent and selective inhibitors of cathepsin B through structure-based drug design., Greenspan PD, Clark KL, Tommasi RA, Cowen SD, McQuire LW, Farley DL, van Duzer JH, Goldberg RL, Zhou H, Du Z, Fitt JJ, Coppa DE, Fang Z, Macchia W, Zhu L, Capparelli MP, Goldstein R, Wigg AM, Doughty JR, Bohacek RS, Knap AK, J Med Chem 2001 Dec 20;44(26):4524-34. PMID:11741472
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (138 Kb) [Save to disk]
  • Biological Unit Coordinates (1gmy.pdb1.gz) 46 Kb
  • Biological Unit Coordinates (1gmy.pdb2.gz) 46 Kb
  • Biological Unit Coordinates (1gmy.pdb3.gz) 47 Kb
  • LPC: Ligand-Protein Contacts for 1GMY
  • CSU: Contacts of Structural Units for 1GMY
  • Likely Quarternary Molecular Structure file(s) for 1GMY
  • Structure Factors (501 Kb)
  • Retrieve 1GMY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1GMY from S2C, [Save to disk]
  • Re-refined 1gmy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1GMY 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 1GMY
  • 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 1GMY, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1gmya_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1gmyb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1gmyc_, region C [Jmol] [rasmolscript] [script source]
  • Fold representative 1gmy 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: [1gmy] [1gmy_C] [1gmy_B] [1gmy_A]
  • SWISS-PROT database: [P07858]
  • Domain organization of [CATB_HUMAN] by SWISSPFAM
  • Domain found in 1GMY: [Pept_C1 ] by SMART
  • Other resources with information on 1GMY
  • Community annotation for 1GMY 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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