1NB5

Crystal structure of stefin A in complex with cathepsin H


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of stefin A in complex with cathepsin H: N-terminal residues of inhibitors can adapt to the active sites of endo- and exopeptidases

Jenko, S.Dolenc, I.Guncar, G.Dobersek, A.Podobnik, M.Turk, D.

(2003) J.Mol.Biol. 326: 875-885

  • Primary Citation of Related Structures:  1NB3

  • PubMed Abstract: 
  • Binding of cystatin-type inhibitors to papain-like exopeptidases cannot be explained by the stefin B-papain complex. The crystal structure of human stefin A bound to an aminopeptidase, porcine cathepsin H, has been determined in monoclinic and orthor ...

    Binding of cystatin-type inhibitors to papain-like exopeptidases cannot be explained by the stefin B-papain complex. The crystal structure of human stefin A bound to an aminopeptidase, porcine cathepsin H, has been determined in monoclinic and orthorhombic crystal forms at 2.8A and 2.4A resolutions, respectively. The asymmetric unit of each form contains four complexes. The structures are similar to the stefin B-papain complex, but with a few distinct differences. On binding, the N-terminal residues of stefin A adopt the form of a hook, which pushes away cathepsin H mini-chain residues and distorts the structure of the short four residue insertion (Lys155A-Asp155D) unique to cathepsin H. Comparison with the structure of isolated cathepsin H shows that the rims of the cathepsin H structure are slightly displaced (up to 1A) from their position in the free enzyme. Furthermore, comparison with the stefin B-papain complex showed that molecules of stefin A bind about 0.8A deeper into the active site cleft of cathepsin H than stefin B into papain. The approach of stefin A to cathepsin H induces structural changes along the interaction surface of both molecules, whereas no such changes were observed in the stefin B-papain complex. Carboxymethylation of papain seems to have prevented the formation of the genuine binding geometry between a papain-like enzyme and a cystatin-type inhibitor as we observe it in the structure presented here.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Jozef Stefan Institute, Jamova 39, SI-1111 Ljubljana, Slovenia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cathepsin H
A, B, C, D
220Sus scrofaGene Names: CTSH
EC: 3.4.22.16
Find proteins for O46427 (Sus scrofa)
Go to Gene View: CTSH
Go to UniProtKB:  O46427
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cathepsin H MINI CHAIN
P, R, S, T
8Sus scrofaGene Names: CTSH
EC: 3.4.22.16
Find proteins for O46427 (Sus scrofa)
Go to Gene View: CTSH
Go to UniProtKB:  O46427
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
STEFIN A
I, J, K, L
98Homo sapiensGene Names: CSTA (STF1, STFA)
Find proteins for P01040 (Homo sapiens)
Go to Gene View: CSTA
Go to UniProtKB:  P01040
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, B, C, D
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.235 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 91.629α = 90.00
b = 97.575β = 90.00
c = 162.188γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SCALEPACKdata scaling
MAINrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-02-18
    Type: Initial release
  • Version 1.1: 2008-04-28
    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