1LYW Aspartic Protease date Jun 30, 1998
title Cathepsin D At Ph 7.5
authors A.Y.Lee, S.V.Gulnik, J.W.Erickson
compound source
Molecule: Cathepsin D
Chain: A, C, E, G
Ec: 3.4.23.5
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Liver

Molecule: Cathepsin D
Chain: B, D, F, H
Ec: 3.4.23.5

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Liver
symmetry Space Group: P 21 21 2
R_factor 0.195 R_Free 0.257
crystal
cell
length a length b length c angle alpha angle beta angle gamma
140.256 136.797 140.416 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand EPE enzyme Hydrolase E.C.3.4.23.5 BRENDA
related structures by homologous chain: 1LYA
Gene
Ontology
ChainFunctionProcessComponent
F, A, E, B, H, C, D, G


Primary referenceConformational switching in an aspartic proteinase., Lee AY, Gulnik SV, Erickson JW, Nat Struct Biol 1998 Oct;5(10):866-71. PMID:9783744
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (286 Kb) [Save to disk]
  • Biological Unit Coordinates (1lyw.pdb1.gz) 75 Kb
  • Biological Unit Coordinates (1lyw.pdb2.gz) 73 Kb
  • Biological Unit Coordinates (1lyw.pdb3.gz) 73 Kb
  • Biological Unit Coordinates (1lyw.pdb4.gz) 73 Kb
  • Biological Unit Coordinates (1lyw.pdb5.gz) 277 Kb
  • Biological Unit Coordinates (1lyw.pdb6.gz) 282 Kb
  • Biological Unit Coordinates (1lyw.pdb7.gz) 141 Kb
  • Biological Unit Coordinates (1lyw.pdb8.gz) 143 Kb
  • Biological Unit Coordinates (1lyw.pdb9.gz) 141 Kb
  • LPC: Ligand-Protein Contacts for 1LYW
  • CSU: Contacts of Structural Units for 1LYW
  • Likely Quarternary Molecular Structure file(s) for 1LYW
  • Retrieve 1LYW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1LYW from S2C, [Save to disk]
  • View 1LYW 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 1LYW
  • 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 1LYW, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1lyw.1, region A:,B [Jmol] [rasmolscript] [script source]
        - Domain d1lyw.2, region C:,D [Jmol] [rasmolscript] [script source]
        - Domain d1lyw.3, region E:,F [Jmol] [rasmolscript] [script source]
        - Domain d1lyw.4, region G:,H [Jmol] [rasmolscript] [script source]
  • Fold representative 1lyw 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: [1lyw_A] [1lyw_E] [1lyw_D] [1lyw_G] [1lyw_F] [1lyw_C] [1lyw_B] [1lyw] [1lyw_H]
  • SWISS-PROT database: [P07339]
  • Domain organization of [CATD_HUMAN] by SWISSPFAM
  • Other resources with information on 1LYW
  • Community annotation for 1LYW 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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