2IPP | pdb_00002ipp

Crystal Structure of the tetragonal form of human liver cathepsin B

• PDB DOI: https://doi.org/10.2210/pdb2IPP/pdb

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


• Deposited: 2006-10-12 Released: 2006-12-12 
• Deposition Author(s): Huber, C.P., Campbell, R.L., Hasnain, S., Hirama, T., To, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Observed: 
  0.157 (Depositor) 

Literature

Crystal Structure of the tetragonal form of human liver cathepsin B

Huber, C.P., Campbell, R.L., Hasnain, S., Hirama, T., To, R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 27.76 kDa 
• Atom Count: 2,097 
• Modeled Residue Count: 252 
• Deposited Residue Count: 252 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin B	A	47	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin B	B	205	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PYS	C [auth A]	2-PYRIDINETHIOL C5 H5 N S WHMDPDGBKYUEMW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Observed: 0.157 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.58	α = 90
b = 85.58	β = 90
c = 34.39	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
PROLSQ	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-12 
Deposition Author(s): Huber, C.P., Campbell, R.L., Hasnain, S., Hirama, T., To, R.

Revision History  

• Version 1.0: 2006-12-12
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary