3RO0

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.1 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:  
    3RNZ, 3RO0, 3RO1

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pyrrolidone-carboxylate peptidaseABCD223Bacillus amyloliquefaciensMutation(s): 2 
Gene Names: pcp
EC: 3.4.19.3
Find proteins for P46107 (Bacillus amyloliquefaciens)
Explore P46107 
Go to UniProtKB:  P46107
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TPT
Query on TPT

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: 1.50 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 290.32α = 90
b = 45.52β = 91.48
c = 67.99γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-05
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection, Database references