5L4R | pdb_00005l4r

X-ray structure of the adduct between thaumatin and cisplatin

• PDB DOI: https://doi.org/10.2210/pdb5L4R/pdb

• Classification: PLANT PROTEIN
• Organism(s): Thaumatococcus daniellii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-05-26 Released: 2016-12-07 
• Deposition Author(s): Russo Krauss, I., Ferraro, G., Merlino, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.154 (Depositor), 0.144 (DCC) 
• R-Value Work: 
  0.112 (Depositor) 
• R-Value Observed: 
  0.114 (Depositor) 

Starting Model: experimental

Literature

Cisplatin-Protein Interactions: Unexpected Drug Binding to N-Terminal Amine and Lysine Side Chains.

Russo Krauss, I., Ferraro, G., Merlino, A.

(2016) Inorg Chem 55: 7814-7816

• PubMed: 27482735 
• DOI: https://doi.org/10.1021/acs.inorgchem.6b01234
• Primary Citation Related Structures: 
  5L4R


• PubMed Abstract: 
  

  Literature studies carried out by mass spectrometry and X-ray crystallography have demonstrated that cisplatin is able to bind proteins mainly close to Met, His, and free Cys side chains. To identify possible alternative modes of cisplatin binding to proteins at the molecular level, here we have solved the high-resolution X-ray structure of the adduct formed in the reaction between the drug and the model protein thaumatin, which does not contain any His and free Cys residues and possesses just one buried Met. Our data reveal unexpected cisplatin binding sites on the protein surface that could have general significance: cisplatin fragments -[Pt(NH3)2Cl](+), -[Pt(NH3)Cl2], and -[Pt(NH3)2(OH2)](2+) bind to a protein N-terminus and close to Lys and Glu side chains.

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Organizational Affiliation: 
• Department of Chemical Sciences, University of Naples Federico II , Via Cintia, I-80126 Naples, Italy.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 25.86 kDa 
• Atom Count: 2,132 
• Modeled Residue Count: 207 
• Deposited Residue Count: 207 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thaumatin-1	A	207	Thaumatococcus daniellii	Mutation(s): 0
UniProt
Find proteins for P02883 (Thaumatococcus daniellii) Explore P02883  Go to UniProtKB:  P02883

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CPT	E [auth A], G [auth A], H [auth A], I [auth A], K [auth A], L [auth A], M [auth A], N [auth A]	Cisplatin Cl2 H6 N2 Pt LXZZYRPGZAFOLE-UHFFFAOYSA-L
73M	D [auth A], F [auth A], J [auth A]	bis(azanyl)-chloranyl-oxidanyl-platinum Cl H5 N2 O Pt DOKMFIMZADYDDQ-UHFFFAOYSA-L
TLA	B [auth A], C [auth A]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
GOL	O [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.154 (Depositor), 0.144 (DCC) 
• R-Value Work:  0.112 (Depositor) 
• R-Value Observed: 0.114 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.837	α = 90
b = 57.837	β = 90
c = 150.159	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-07 
Deposition Author(s): Russo Krauss, I., Ferraro, G., Merlino, A.

Revision History  

• Version 1.0: 2016-12-07
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary