2DCB

X-ray crystal structure analysis of bovine spleen cathepsin B-CA076 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.183 

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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CATHEPSIN B
A
256Bos taurusMutation(s): 0 
Gene Names: CTSB
EC: 3.4.22.1
Find proteins for P07688 (Bos taurus)
Go to Gene View: CTSB
Go to UniProtKB:  P07688
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
76V
Query on 76V

Download SDF File 
Download CCD File 
A
N-{[(2S,3S)-3-(ETHOXYCARBONYL)OXIRAN-2-YL]CARBONYL}-L-ISOLEUCYL-L-ISOLEUCINE
CA076, N-(L-3-TRANS-ETHOXYCARBONYLOXIRANE-2-CARBONYL)-L-ISOLEUCYL-L-ISOLEUCINE
C18 H30 N2 O7
CFABOFMUPCWOPC-LHEWDLALSA-N
 Ligand Interaction
PO4
Query on PO4

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

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.183 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 72.440α = 90.00
b = 72.440β = 90.00
c = 140.000γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description