2PBH

CRYSTAL STRUCTURE OF HUMAN PROCATHEPSIN B AT 3.3 ANGSTROM RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb2PBH/pdb

• Classification: THIOL PROTEASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-02-14 Released: 1998-02-25 
• Deposition Author(s): Podobnik, M., Turk, D., Kuhelj, R., Turk, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.269 
• R-Value Work: 0.231 

Starting Model: experimental

Literature

Crystal structures of human procathepsin B at 3.2 and 3.3 Angstroms resolution reveal an interaction motif between a papain-like cysteine protease and its propeptide.

Turk, D., Podobnik, M., Kuhelj, R., Dolinar, M., Turk, V.

(1996) FEBS Lett 384: 211-214

• PubMed: 8617355 
• DOI: https://doi.org/10.1016/0014-5793(96)00309-2
• Primary Citation of Related Structures:  
  1PBH, 2PBH


• PubMed Abstract: 
  

  A wild-type human procathepsin B was expressed, crystallized in two crystal forms and its crystal structure determined at 3.2 and 3.3 Angstroms resolution. The structure reveals that the propeptide folds on the cathepsin B surface, shielding the enzyme active site from exposure to solvent. The structure of the enzymatically active domains is virtually identical to that of the native enzyme [Musil et al. (1991) EMBO J. 10, 2321-2330]: the main difference is that the occluding loop residues are lifted above the body of the mature enzyme, supporting the propeptide structure.

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Organizational Affiliation: 

Dept of Biochem. and Mol. Biol. Jozef Stefan Institute, Ljubljana, Slovenia.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 35.23 kDa 
• Atom Count: 2,470 
• Modelled Residue Count: 317 
• Deposited Residue Count: 317 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROCATHEPSIN B	A	317	Homo sapiens	Mutation(s): 0  EC: 3.4.22.1
UniProt & NIH Common Fund Data Resources
Find proteins for P07858 (Homo sapiens) Explore P07858  Go to UniProtKB:  P07858
PHAROS:  P07858 GTEx:  ENSG00000164733

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.269 
• R-Value Work: 0.231 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.75	α = 90
b = 78.75	β = 90
c = 153.64	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
CCP4	data reduction
MAIN	model building
MAIN	refinement
CCP4	data scaling
MAIN	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-02-25 
Deposition Author(s): Podobnik, M., Turk, D., Kuhelj, R., Turk, V.

Revision History  

• Version 1.0: 1998-02-25
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-04-03
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-09
  Changes: Structure summary