2DC7

X-ray crystal structure analysis of bovine spleen cathepsin B-CA042 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.214
  • R-Value Work: 0.187

Literature

Macromolecules
Sequence Display for 2DC7

Classification: HYDROLASE

Total Structure Weight: 28480.49

Macromolecule Entities
Molecule Chains Length Organism Details
CATHEPSIN B A 256 Bos taurus EC#: 3.4.22.1 IUBMB
Gene Name(s): CTSB Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
042
Query on 042

A N-{[(2S,3S)-3-(ETHOXYCARBONYL)OXIRAN-2-YL]CARBONYL}- L-THREONYL-L-ISOLEUCINE
CA042, N-(L-3-TRANS-ETHOXYCARBONYLOXIRANE- 2-CARBONYL)-L-THREONYL-L-ISOLEUCINE (Synonym)
C16 H26 N2 O8
QMPAEYUADYAXIX-XFVKVHEMSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.214
  • R-Value Work: 0.187
  • Space Group: P 43 21 2

Unit Cell:

Length (Å) Angle (°)
a = 72.32 α = 90.00
b = 72.32 β = 90.00
c = 139.83 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-12-31
  • 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