1LYB

CRYSTAL STRUCTURES OF NATIVE AND INHIBITED FORMS OF HUMAN CATHEPSIN D: IMPLICATIONS FOR LYSOSOMAL TARGETING AND DRUG DESIGN

Structural Biology Knowledgebase: 1LYB SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Observed: 0.179

Literature

Macromolecules
Sequence Display for 1LYB

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 77230.37

Macromolecule Entities
Molecule Chains Length Organism Details
CATHEPSIN D A, C 97 Homo sapiens EC#: 3.4.23.5 IUBMB
Gene Name(s): CTSD Gene View CPSD
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CATHEPSIN D B, D 241 Homo sapiens EC#: 3.4.23.5 IUBMB
Gene Name(s): CTSD Gene View CPSD
PEPSTATIN I, J 6 Streptomyces argenteolus

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

A, B, C, D N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

A, C BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

A, C ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000557
Query on PRD_000557
I, J Pepstatin Oligopeptide /
Enzyme Inhibitor
Ligand Explorer

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Observed: 0.179
  • Space Group: P 65

Unit Cell:

Length (Å) Angle (°)
a = 125.90 α = 90.00
b = 125.90 β = 90.00
c = 104.10 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1993-04-22
  • Released Date: 1994-01-31
  • Deposition author(s): Baldwin, E.T., Bhat, T.N., Gulnik, S., Erickson, J.W.

Revision History

  • 2013-02-27
    Type: Other | Details: Add PRD info
  • 2011-07-13
    Type: Linkage | Details: Linkage
  • 2011-07-13
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-13
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-13
    Type: Binding sites and description | Details: Binding sites and description
  • 2011-07-13
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-13
    Type: Function and keywords | Details: Function and keywords
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4