cut-1b; NCN-Pt-Pincer-Cutinase Hybrid

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

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Solid-state structural characterization of cutinase-ECE-pincer-metal hybrids

Rutten, L.Wieczorek, B.Mannie, J.P.B.A.Kruithof, C.A.Dijkstra, H.P.Egmond, M.R.Lutz, M.Klein Gebbink, R.J.M.Gros, P.van Koten, G.

(2009) Chemistry 15: 4270-4280

  • DOI: https://doi.org/10.1002/chem.200801995
  • Primary Citation of Related Structures:  
    3EF3, 3ESA, 3ESB, 3ESC, 3ESD

  • PubMed Abstract: 

    The first crystal structures of lipases that have been covalently modified through site-selective inhibition by different organometallic phosphonate-pincer-metal complexes are described. Two ECE-pincer-type d(8)-metal complexes, that is, platinum (1) or palladium (2) with phosphonate esters (ECE = [(EtO)-(O=)P(-O-C(6)H(4)-(NO(2))-4)(-C(3)H(6)-4-(C(6)H(2)-(CH(2)E)(2))](-); E = NMe(2) or SMe) were introduced prior to crystallization and have been shown to bind selectively to the Ser(120) residue in the active site of the lipase cutinase to give cut-1 (platinum) or cut-2 (palladium) hybrids. For all five presented crystal structures, the ECE-pincer-platinum or -palladium head group sticks out of the cutinase molecule and is exposed to the solvent. Depending on the nature of the ECE-pincer-metal head group, the ECE-pincer-platinum and -palladium guests occupy different pockets in the active site of cutinase, with concomitant different stereochemistries on the phosphorous atom for the cut-1 (S(P)) and cut-2 (R(P)) structures. When cut-1 was crystallized under halide-poor conditions, a novel metal-induced dimeric structure was formed between two cutinase-bound pincer-platinum head groups, which are interconnected through a single mu-Cl bridge. This halide-bridged metal dimer shows that coordination chemistry is possible with protein-modified pincer-metal complexes. Furthermore, we could use NCN-pincer-platinum complex 1 as site-selective tool for the phasing of raw protein diffraction data, which shows the potential use of pincer-platinum complex 1 as a heavy-atom derivative in protein crystallography.

  • Organizational Affiliation

    Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cutinase 1
A, B
214Fusarium vanetteniiMutation(s): 1 
Find proteins for P00590 (Fusarium vanettenii)
Explore P00590 
Go to UniProtKB:  P00590
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00590
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NXC

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C23 H33 Cl N3 O5 P Pt
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.97α = 90
b = 71.859β = 96.94
c = 68.568γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Advisory, Database references, Derived calculations
  • Version 1.3: 2023-11-01
    Changes: Data collection, Refinement description