Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 104.26 kDa 
• Atom Count: 7552 
• Residue Count: 902 
• Unique protein chains: 1

1IVY

PHYSIOLOGICAL DIMER HPP PRECURSOR

• DOI: 10.2210/pdb1IVY/pdb

• Classification: CARBOXYPEPTIDASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 1996-06-12 Released: 1997-04-21 
• Deposition Author(s): Rudenko, G., Bonten, E., D'Azzo, A., Hol, W.G.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.268 
• R-Value Work: 0.213 
• R-Value Observed: 0.213 

Literature

Three-dimensional structure of the human 'protective protein': structure of the precursor form suggests a complex activation mechanism.

Rudenko, G., Bonten, E., d'Azzo, A., Hol, W.G.

(1995) Structure 3: 1249-1259

• PubMed: 8591035 
• DOI: 10.1016/s0969-2126(01)00260-x
• Primary Citation of Related Structures:  
  1IVY


• PubMed Abstract: 
  

The human 'protective protein' (HPP) forms a multi-enzyme complex with beta-galactosidase and neuraminidase in the lysosomes, protecting these two glycosidases from degradation. In humans, deficiency of HPP leads to the lysosomal storage disease galactosialidosis. Proteolytic cleavage of the precursor form of HPP involves removal of a 2 kDa excision peptide and results in a carboxypeptidase activity. The physiological relevance of this activity is, as yet, unknown.

---

Related Citations: 

• Structure Determination of the Human Protective Protein: Twofold Averaging Reveals the Three-Dimensional Structure of a Domain which Was Entirely Absent in the Initial Model
  Rudenko, G., Bonten, E., D'Azzo, A., Hol, W.G.J.
  (1996) Acta Crystallogr D Biol Crystallogr 52: 923

• Expression of Cdna Encoding the Human 'Protective Protein' Associated with Lysosomal Beta-Galactosidase and Neuraminidase: Homology to Yeast Proteases
  Galjart, N.J., Gillemans, N., Harris, A., Van Der Horst, G.T., Verheijen, F.W., Galjaard, H., D'Azzo, A.
  (1988) Cell 54: 755

---

Organizational Affiliation: 

Department of Biological Structure, School of Medicine, University of Washington, Seattle 98195-7742, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HUMAN PROTECTIVE PROTEIN	A, B	452	Homo sapiens	Mutation(s): 0  Gene Names: HUPP54, CTSA, PPGB EC: 3.4.16.5
Find proteins for P10619 (Homo sapiens) Explore P10619  Go to UniProtKB:  P10619
NIH Common Fund Data Resources
PHAROS:  P10619 GTEx:  ENSG00000064601

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	2		N-Glycosylation

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, B	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.268 
• R-Value Work: 0.213 
• R-Value Observed: 0.213 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.04	α = 90
b = 148.11	β = 90
c = 80.97	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
ROTAVATA	data reduction
Agrovata	data reduction
TRUNCATE	data reduction
X-PLOR	model building
X-PLOR	refinement
CCP4	data scaling
ROTAVATA	data scaling
TRUNCATE	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1996-06-12 
• Released Date: 1997-04-21 
Deposition Author(s): Rudenko, G., Bonten, E., D'Azzo, A., Hol, W.G.J.

Revision History 

• Version 1.0: 1997-04-21
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Refinement description, Structure summary