1LYB Hydrolase Hydrolase Inhibitor date Apr 22, 1993
title Crystal Structures Of Native And Inhibited Forms Of Human Ca Implications For Lysosomal Targeting And Drug Design
authors E.T.Baldwin, T.N.Bhat, S.Gulnik, J.W.Erickson
compound source
Molecule: Cathepsin D
Chain: A, C
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Liver
Tissue: Liver

Molecule: Cathepsin D
Chain: B, D

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Liver
Tissue: Liver

Molecule: Pepstatin
Chain: I, J
Engineered: Yes

Organism_scientific: Streptomyces Argenteolus Subsp. Toyona
Organism_taxid: 285516
symmetry Space Group: P 65
R_factor 0.179 R_Free NULL
length a length b length c angle alpha angle beta angle gamma
125.900 125.900 104.100 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.50 Å
ligand BMA, IVA, MAN, NAG, STA enzyme Hydrolase E.C. BRENDA
note 1LYB (Molecule of the Month:pdb12)
related structures by homologous chain: 1LYA, 1QDM
A, D, C, B

Primary referenceCrystal structures of native and inhibited forms of human cathepsin D: implications for lysosomal targeting and drug design., Baldwin ET, Bhat TN, Gulnik S, Hosur MV, Sowder RC 2nd, Cachau RE, Collins J, Silva AM, Erickson JW, Proc Natl Acad Sci U S A 1993 Jul 15;90(14):6796-800. PMID:8393577
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (140 Kb) [Save to disk]
  • Biological Unit Coordinates (1lyb.pdb1.gz) 133 Kb
  • Biological Unit Coordinates (1lyb.pdb2.gz) 68 Kb
  • Biological Unit Coordinates (1lyb.pdb3.gz) 68 Kb
  • LPC: Ligand-Protein Contacts for 1LYB
  • CSU: Contacts of Structural Units for 1LYB
  • Likely Quarternary Molecular Structure file(s) for 1LYB
  • Retrieve 1LYB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1LYB from S2C, [Save to disk]
  • View 1LYB 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 1LYB
  • 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 1LYB, from MSDmotif at EBI
  • Genome occurence of 1LYB's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1lyb.1, region A:,B [Jmol] [rasmolscript] [script source]
        - Domain d1lyb.2, region C:,D [Jmol] [rasmolscript] [script source]
  • Fold representative 1lyb 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: [1lyb_I] [1lyb_C] [1lyb_B] [1lyb] [1lyb_J] [1lyb_D] [1lyb_A]
  • SWISS-PROT database: [P07339]
  • Domain organization of [CATD_HUMAN] by SWISSPFAM
  • Other resources with information on 1LYB
  • Community annotation for 1LYB at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Domain movements in 1LYB from the Database of Macromolecular Movements.
  • Images from IMB Jena Image Library of Biological Macromolecules.

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