Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

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

Biological Assembly 2  

 3D View: Structure | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 56048.32 
• Atom Count: 3928 
• Residue Count: 504 
• Unique protein chains: 2

1CSB

Crystal structure of cathepsin b inhibited with CA030 at 2.1 angstroms resolution: A basis for the design of specific epoxysuccinyl inhibitors

• DOI: 10.2210/pdb1CSB/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens


• Deposited: 1994-12-09 Released: 1996-04-03 
• Deposition Author(s): Turk, D., Bode, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Work: 0.194 

Literature

Crystal structure of cathepsin B inhibited with CA030 at 2.0-A resolution: A basis for the design of specific epoxysuccinyl inhibitors.

Turk, D., Podobnik, M., Popovic, T., Katunuma, N., Bode, W., Huber, R., Turk, V.

(1995) Biochemistry 34: 4791-4797

• PubMed: 7718586 


• PubMed Abstract: 
  

Crystals of cysteine protease human cathepsin B inhibited with CA030 (ethyl ester of epoxysuccinyl-Ile-Pro-OH) [Murata, M., et al. (1991) FEBS Lett. 280, 307-310; Towatari, T., et al. (1991) FEBS Lett. 280, 311-315] were isomorphous to a previous published structure of cathepsin B [Musil, D., et al. (1991) EMBO J. 10, 2321-2330]. The crystal structure of the complex was refined at 2.0-A resolution to an R-value of 0.194. CA030 is well-defined in the electron density. The Ile-Pro-OH part of CA030 mimics a substrate P1' and P2' residues. The structure thus reveals for the first time a substratelike interaction in the S1' and S2' sites of a papain-like cysteine protease. The CA030 ethyl ester group occupies the S2 site. The structure confirms the role of residues His 110 and His 111 as the receptors of a peptidic substrate C-terminal carboxylic group. The structure suggests that an epoxysuccinyl fragment can be used to extend binding into primed and nonprimed substrate binding sites of a papain-like cysteine protease.

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Related Citations: 

• The Refined 2.15 Angstrom X-Ray Crystal Structure of Human Liver Cathepsin B: The Structural Basis for its Specificity
  Musil, D.,Zucic, D.,Turk, D.,Engh, R.A.,Mayr, I.,Huber, R.,Popovic, T.,Turk, V.,Towatari, T.,Katunuma, N.,Bode, W.
  (1991) Embo J. 10: 2321




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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, Jozef Stefan Institute, Ljubljana, Slovenia.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
CATHEPSIN B light chain	A, D	47	Homo sapiens	Mutation(s): 0  Gene Names: CTSB (CPSB) EC: 3.4.22.1
Find proteins for P07858 (Homo sapiens) Go to Gene View: CTSB Go to UniProtKB:  P07858

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
CATHEPSIN B heavy chain	B, E	205	Homo sapiens	Mutation(s): 0  Gene Names: CTSB (CPSB) EC: 3.4.22.1
Find proteins for P07858 (Homo sapiens) Go to Gene View: CTSB Go to UniProtKB:  P07858

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
EP0	A, E	N-[(3R)-4-ethoxy-3-hydroxy-4-oxobutanoyl]-L-isoleucyl-L-proline epoxy succinyl inhibitor C17 H28 N2 O7 XMBVSOIOHZNPHI-FMSGJZPZSA-N

Biologically Interesting Molecules 1 Unique
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000310 (EP0)	A,E	CA030, ethyl ester of epoxysuccinyl-Ile-Pro-OH	Peptide-like / Inhibitor		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Work: 0.194 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 86.510	α = 90.00
b = 34.150	β = 103.10
c = 85.530	γ = 90.00

Software Package:

Software Name	Purpose
X-PLOR	refinement
XDS	data scaling
X-PLOR	model building
X-PLOR	phasing
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1994-12-09 
• Released Date: 1996-04-03 
• Deposition Author(s): Turk, D., Bode, W.

Revision History 

• Version 1.0: 1996-04-03
  Type: Initial release
• Version 1.1: 2008-03-24
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2011-08-31
  Type: Non-polymer description
• Version 1.4: 2012-12-12
  Type: Other