2DCD

X-ray crystal structure analysis of bovine spleen cathepsin B-CA078 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Quantitative estimation of each active subsite of cathepsin B for the inhibitory activity, based on the inhibitory activitybinding mode relationship of a series of epoxysuccinyl inhibitors by X-ray crystal structure analyses of the complexes

Watanabe, D.Yamamoto, A.Matsumoto, K.Murata, M.Kitamura, K.Tomoo, K.Ishida, T.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CATHEPSIN BA256Bos taurusMutation(s): 0 
Gene Names: CTSB
EC: 3.4.22.1
Find proteins for P07688 (Bos taurus)
Explore P07688 
Go to UniProtKB:  P07688
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
78A
Query on 78A

Download CCD File 
A
N-({(2S,3S)-3-[(BENZYLAMINO)CARBONYL]OXIRAN-2-YL}CARBONYL)-L-ISOLEUCYL-L-PROLINE
C22 H29 N3 O6
MERYMLLGRCNRKE-HILJTLORSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
78AIC50:  29   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.26α = 90
b = 72.26β = 90
c = 140γ = 90
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2006-01-01 
  • Released Date: 2006-01-24 
  • Deposition Author(s): Watanabe, D.

Revision History 

  • Version 1.0: 2006-01-24
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description