8BRC

Crystal structure of the adduct between human serum transferrin and cisplatin

• PDB DOI: https://doi.org/10.2210/pdb8BRC/pdb

• Classification: METAL TRANSPORT
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2022-11-22 Released: 2023-01-18 
• Deposition Author(s): Troisi, R., Galardo, F., Ferraro, G., Sica, F., Merlino, A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.17 Å
• R-Value Free: 0.243 
• R-Value Work: 0.177 
• R-Value Observed: 0.181 

Starting Model: experimental

Literature

Cisplatin Binding to Human Serum Transferrin: A Crystallographic Study.

Troisi, R., Galardo, F., Ferraro, G., Sica, F., Merlino, A.

(2023) Inorg Chem 62: 675-678

• PubMed: 36602395 
• DOI: https://doi.org/10.1021/acs.inorgchem.2c04206
• Primary Citation of Related Structures:  
  8BRC


• PubMed Abstract: 
  

  The molecular mechanism of how human serum transferrin (hTF) recognizes cisplatin at the atomic level is still unclear. Here, we report the molecular structure of the adduct formed upon the reaction of hTF with cisplatin. Pt binds the side chain of Met256 (at the N-lobe), without altering the protein overall conformation.

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Organizational Affiliation: 

Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, via Cintia, Naples I-80126, Italy.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 75.91 kDa 
• Atom Count: 5,264 
• Modelled Residue Count: 670 
• Deposited Residue Count: 679 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serotransferrin	A	679	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P02787 (Homo sapiens) Explore P02787  Go to UniProtKB:  P02787
PHAROS:  P02787 GTEx:  ENSG00000091513
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P02787-1

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PT (Subject of Investigation/LOI)	E [auth A]	PLATINUM (II) ION Pt HRGDZIGMBDGFTC-UHFFFAOYSA-N
MLI	C [auth A]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
FE	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
NH3 (Subject of Investigation/LOI)	F [auth A], G [auth A]	AMMONIA H3 N QGZKDVFQNNGYKY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.17 Å
• R-Value Free: 0.243 
• R-Value Work: 0.177 
• R-Value Observed: 0.181 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.34	α = 90
b = 156.4	β = 90
c = 107.44	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
autoPROC	data processing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-01-18 
Deposition Author(s): Troisi, R., Galardo, F., Ferraro, G., Sica, F., Merlino, A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-01-18
  Type: Initial release
  
• Version 1.1: 2023-01-25
  Changes: Database references
• Version 1.2: 2024-02-07
  Changes: Data collection