3RO0

Crystal structure of Bacillus amyloliquefaciens pyroglutamyl peptidase I and terpyridine platinum(II)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Terpyridine Platinum(II) Complexes Inhibit Cysteine Proteases by Binding to Active-site Cysteine

Lo, Y.-C.Su, W.-C.Ko, T.-P.Wang, N.-C.Wang, A.H.-J.

(2011) J.Biomol.Struct.Dyn. 29: 267-282

  • DOI: 10.1080/073911011010524993
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Platinum(II) complexes have been demonstrated to form covalent bonds with sulfur-donating ligands (in glutathione, metallothionein and other sulfur-containing biomolecules) or coordination bonds with nitrogen-donating ligands (such as histidine and g ...

    Platinum(II) complexes have been demonstrated to form covalent bonds with sulfur-donating ligands (in glutathione, metallothionein and other sulfur-containing biomolecules) or coordination bonds with nitrogen-donating ligands (such as histidine and guanine). To investigate how these compounds interact with cysteine proteases, we chose terpyridine platinum(II) (TP-Pt(II)) complexes as a model system. By using X-ray crystallography, we demonstrated that TP-Pt(II) formed a covalent bond with the catalytic cysteine residue in pyroglutamyl peptidase I. Moreover, by using MALDI (matrix-assisted laser desorption/ionization) and TOF-TOF (time of flight) mass spectrometry, we elucidated that the TP-Pt(II) complex formed a covalent bond with the active-site cysteine residue in two other types of cysteine protease. Taken together, the results unequivocally showed that TP-Pt(II) complexes can selectively bind to the active site of most cysteine proteases. Our findings here can be useful in the design of new anti-cancer, anti-parasite or anti-virus platinum(II) compounds.


    Organizational Affiliation

    Department and Institute of Pharmacology, National Yang-Ming University, Taipei 112, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyrrolidone-carboxylate peptidase
A, B, C, D
223Bacillus amyloliquefaciensMutation(s): 2 
Gene Names: pcp
EC: 3.4.19.3
Find proteins for P46107 (Bacillus amyloliquefaciens)
Go to UniProtKB:  P46107
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TPT
Query on TPT

Download SDF File 
Download CCD File 
A, B, C, D
2,2':6',2''-TERPYRIDINE PLATINUM(II) Chloride
C15 H11 Cl N3 Pt
XTQMQLRZXBEQCS-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TPTIC50: 31890 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.179 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 290.320α = 90.00
b = 45.520β = 91.48
c = 67.990γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-05
    Type: Initial release