1LYB
CRYSTAL STRUCTURES OF NATIVE AND INHIBITED FORMS OF HUMAN CATHEPSIN D: IMPLICATIONS FOR LYSOSOMAL TARGETING AND DRUG DESIGN
- PDB DOI: https://doi.org/10.2210/pdb1LYB/pdb
- Classification: HYDROLASE/HYDROLASE INHIBITOR
- Organism(s): Homo sapiens, Streptomyces argenteolus subsp. toyonakensis
- Mutation(s): No 
- Membrane Protein: Yes  OPM
- Deposited: 1993-04-22 Released: 1994-01-31 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Work: 0.179 
- R-Value Observed: 0.179 
wwPDB Validation   3D Report Full Report
This is version 3.0 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
CATHEPSIN D | A, D [auth C] | 97 | Homo sapiens | Mutation(s): 0  EC: 3.4.23.5 Membrane Entity: Yes  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P07339 (Homo sapiens) Explore P07339  Go to UniProtKB:  P07339 | |||||
PHAROS:  P07339 GTEx:  ENSG00000117984  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P07339 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
CATHEPSIN D | B, E [auth D] | 241 | Homo sapiens | Mutation(s): 0  EC: 3.4.23.5 Membrane Entity: Yes  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P07339 (Homo sapiens) Explore P07339  Go to UniProtKB:  P07339 | |||||
PHAROS:  P07339 GTEx:  ENSG00000117984  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P07339 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by: Sequence | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
PEPSTATIN | C [auth I], F [auth J] | 6 | Streptomyces argenteolus subsp. toyonakensis | Mutation(s): 0  | |
Sequence AnnotationsExpand | |||||
|
Oligosaccharides
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | G [auth E], H [auth F] | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G22573RC GlyCosmos:  G22573RC GlyGen:  G22573RC |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | I [auth B], J [auth D] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3 | |||||
---|---|---|---|---|---|
ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_000557 Query on PRD_000557 | C [auth I], F [auth J] | Pepstatin | Oligopeptide / Enzyme inhibitor |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Work: 0.179 
- R-Value Observed: 0.179 
- Space Group: P 65
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 125.9 | α = 90 |
b = 125.9 | β = 90 |
c = 104.1 | γ = 120 |
Software Name | Purpose |
---|---|
X-PLOR | model building |
X-PLOR | refinement |
X-PLOR | phasing |
Entry History 
Deposition Data
- Released Date: 1994-01-31  Deposition Author(s): Baldwin, E.T., Bhat, T.N., Gulnik, S., Erickson, J.W.
Revision History (Full details and data files)
- Version 1.0: 1994-01-31
Type: Initial release - Version 1.1: 2008-03-03
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance - Version 1.3: 2013-02-27
Changes: Other - Version 1.4: 2017-11-29
Changes: Derived calculations, Other - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 3.0: 2023-11-15
Changes: Atomic model, Data collection, Database references, Structure summary