1IVY

PHYSIOLOGICAL DIMER HPP PRECURSOR

• PDB DOI: https://doi.org/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.

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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: https://doi.org/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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
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: 7,552 
• Modelled Residue Count: 902 
• Deposited Residue Count: 904 
• Unique protein chains: 1

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 EC: 3.4.16.5
UniProt & NIH Common Fund Data Resources
Find proteins for P10619 (Homo sapiens) Explore P10619  Go to UniProtKB:  P10619
PHAROS:  P10619 GTEx:  ENSG00000064601

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G07375KG GlyCosmos:  G07375KG GlyGen:  G07375KG

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], F [auth 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

• 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
• Version 2.1: 2024-04-03
  Changes: Data collection, Database references, Refinement description, Structure summary