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 Ec: 3.4.23.5		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Organ: Liver Tissue: Liver
Molecule: Cathepsin D Chain: B, D Ec: 3.4.23.5		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
crystal cell	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 Diffraction	resolution	2.50 Å
ligand	BMA, IVA, MAN, NAG, STA	enzyme	Hydrolase E.C.3.4.23.5 BRENDA
note	1LYB (Molecule of the Month:pdb12)
related structures	by homologous chain: 1LYA, 1QDM
Gene Ontology	Chain Function Process Component A, D, C, B
Primary reference	Crystal 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

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server 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] 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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