6ZSR | pdb_00006zsr

Crystal structure of the Cisplatin beta-Lactoglobulin adduct formed after 72 h of soaking

• PDB DOI: https://doi.org/10.2210/pdb6ZSR/pdb

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


• Deposited: 2020-07-16 Released: 2020-09-30 
• Deposition Author(s): Balasco, N., Ferraro, G., Merlino, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.283 (Depositor), 0.285 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.202 (DCC) 

Starting Model: experimental

Literature

Cisplatin binding to beta-lactoglobulin: a structural study.

Balasco, N., Ferraro, G., Loreto, D., Iacobucci, I., Monti, M., Merlino, A.

(2020) Dalton Trans 49: 12450-12457

• PubMed: 32852026 
• DOI: https://doi.org/10.1039/d0dt02582h
• Primary Citation Related Structures: 
  6ZSQ, 6ZSR


• PubMed Abstract: 
  

  β-Lactoglobulin is a major globular milk whey carrier with potential applications as an oral drug delivery system. Herein, the interactions between β-lactoglobulin and cisplatin are investigated by UV-Vis absorption spectroscopy, circular dichroism, X-ray crystallography and electrospray ionization mass spectrometry. Structural data indicate that the protein retains its conformation upon cisplatin binding. Pt-containing fragments bind the side chains of Met7, His146 and Lys8, with the number of binding sites increasing over time. Mass spectrometry data indicate that [Pt(NH3)2Cl+], [Pt(NH3)2OH22+] and [Pt(NH3)22+] fragments interact with β-lactoglobulin; up to 3 cisplatin fragments can bind the protein and the number of cisplatin binding sites increases over time. This work opens a new pathway in pharmaceutical studies based on a rational design of metal-based drug/β-lactoglobulin adducts as delivering vehicles of metallodrugs.

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Organizational Affiliation: 
• Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, 80134 Napoli, Italy.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 37.8 kDa 
• Atom Count: 2,797 
• Modeled Residue Count: 323 
• Deposited Residue Count: 324 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactoglobulin	A [auth AAA], B [auth BBB]	162	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P02754 (Bos taurus) Explore P02754  Go to UniProtKB:  P02754

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PT (Subject of Investigation/LOI)	D [auth AAA], E [auth AAA], I [auth BBB], J [auth BBB], K [auth BBB]	PLATINUM (II) ION Pt HRGDZIGMBDGFTC-UHFFFAOYSA-N
SO4	G [auth BBB], H [auth BBB]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NH3 (Subject of Investigation/LOI)	C [auth AAA], F [auth BBB]	AMMONIA H3 N QGZKDVFQNNGYKY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.283 (Depositor), 0.285 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.202 (DCC) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.62	α = 70.27
b = 48.8	β = 68.49
c = 49.18	γ = 76.99

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-09-30 
Deposition Author(s): Balasco, N., Ferraro, G., Merlino, A.

Revision History  

• Version 1.0: 2020-09-30
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary