6E2B

Ubiquitin in complex with Pt(2-phenilpyridine)(PPh3)

  • Classification: PROTEIN BINDING
  • Organism(s): Bos taurus
  • Mutation(s): No 

  • Deposited: 2018-07-11 Released: 2018-11-14 
  • Deposition Author(s): Zhemkov, V.A., Kim, M.
  • Funding Organization(s): Russian Science Foundation, Other government

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Reactions of Cyclometalated Platinum(II) [Pt(N∧C)(PR3)Cl] Complexes with Imidazole and Imidazole-Containing Biomolecules: Fine-Tuning of Reactivity and Photophysical Properties via Ligand Design.

Solomatina, A.I.Chelushkin, P.S.Abakumova, T.O.Zhemkov, V.A.Kim, M.Bezprozvanny, I.Gurzhiy, V.V.Melnikov, A.S.Anufrikov, Y.A.Koshevoy, I.O.Su, S.H.Chou, P.T.Tunik, S.P.

(2019) Inorg Chem 58: 204-217

  • DOI: https://doi.org/10.1021/acs.inorgchem.8b02204
  • Primary Citation of Related Structures:  
    6E2B

  • PubMed Abstract: 

    This work describes interaction of a family of [Pt(N C)(PR 3 )Cl] complexes with imidazole (Im), possible application of this chemistry for regioselective labeling of proteins through imidazole rings of histidine residues and employment of the resulting phosphorescent products in bioimaging. It was found that the complexes containing aliphatic phosphines display reversible substitution of chloride ligand for imidazole function that required considerable excess of imidazole to obtain full conversion into the substituted [Pt(ppy)(PR 3 )(Im)] product, whereas the substitution in the complexes with aromatic phosphines readily proceeds in 1:1.5 mixture of reagents. Rapid, selective, and quantitative coordination of imidazole to the platinum complexes enabled regioselective labeling of ubiquitin. X-ray protein crystallography of the {[Pt(ppy)(PPh 3 )]/ubiquitin} conjugate revealed direct bonding of the platinum center to unique histidine-68 residue through the nitrogen atom of imidazole function, the coordination being also supported by noncovalent interaction of the ligands with the protein secondary structure. The variations of the cyclometalating N C ligands gave a series of [Pt(N C)(PPh 3 )Cl] complexes (N C = 2-phenylpyridine, 2-(benzofuran-3-yl)pyridine, 2-(benzo[b]thiophen-3-yl)pyridine, methyl-2-phenylquinoline-4-carboxylate), which were used to investigate the impact of N C-ligand onto photophysical properties of the imidazole complexes and conjugates with human serum albumin (HSA). The chloride ligand substitution for imidazole and formation of the conjugates results in ignition of the platinum chromophore luminescence with substantially higher quantum yield in the latter case. Variation of the metalating N C-ligand made possible the shift of the emission to the red region of visible spectrum for both types of the products. Cell-viability tests revealed low cytotoxicity of all {[Pt(N C)(PPh 3 )Cl]/HSA} conjugates, while PLIM experiments demonstrated their high potential for oxygen sensing.


  • Organizational Affiliation

    Center of Life Sciences , Skolkovo Institute of Science and Technology , Skolkovo, Nobel str. 3 , 143026 Moscow , Russia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin76Bos taurusMutation(s): 0 
UniProt
Find proteins for P62992 (Bos taurus)
Explore P62992 
Go to UniProtKB:  P62992
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62992
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PT7
Query on PT7

Download Ideal Coordinates CCD File 
K [auth A],
N [auth C],
W [auth P]
chloro[2-(pyridin-2-yl-kappaN)phenyl-kappaC~1~](triphenyl-lambda~5~-phosphanyl)platinum(2+)
C29 H23 Cl N P Pt
KHJLZDWNJSEPIZ-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
Q [auth I]
T [auth P]
U [auth P]
G [auth A],
H [auth A],
Q [auth I],
T [auth P],
U [auth P],
V [auth P]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
L [auth C]
M [auth C]
O [auth C]
I [auth A],
J [auth A],
L [auth C],
M [auth C],
O [auth C],
P [auth E],
R [auth I],
S [auth I]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.381α = 90
b = 140.381β = 90
c = 62.447γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Science FoundationRussian Federation16-43-03003
Other governmentRussian Federation17.991.2017/PCh

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-14
    Type: Initial release
  • Version 1.1: 2019-05-01
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description