4S1Y | pdb_00004s1y

X-ray structure of human serum albumin complexed with cisplatin

• PDB DOI: https://doi.org/10.2210/pdb4S1Y/pdb

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


• Deposited: 2015-01-16 Released: 2015-04-29 
• Deposition Author(s): Merlino, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.16 Å
• R-Value Free: 
  0.329 (Depositor), 0.326 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

Cisplatin binding to human serum albumin: a structural study.

Ferraro, G., Massai, L., Messori, L., Merlino, A.

(2015) Chem Commun (Camb) 51: 9436-9439

• PubMed: 25873085 
• DOI: https://doi.org/10.1039/c5cc01751c
• Primary Citation Related Structures: 
  4S1Y


• PubMed Abstract: 
  

  The reaction between cisplatin and human serum albumin (HSA) was investigated by X-ray crystallography and crystal structures of the cisplatin/HSA adduct were eventually solved for the first time. Structural data unambiguously prove that cisplatin mainly binds to His105 and Met329 side chains; additional binding sites are detected at His288, Met298, and Met548 and at His535, His67 and His247.

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Organizational Affiliation: 
• Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126, Napoli, Italy. [e-mail].

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: 68.07 kDa 
• Atom Count: 4,217 
• Modeled Residue Count: 543 
• Deposited Residue Count: 585 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serum albumin	A	585	Homo sapiens	Mutation(s): 0  Gene Names: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341
UniProt & NIH Common Fund Data Resources
Find proteins for P02768 (Homo sapiens) Explore P02768  Go to UniProtKB:  P02768
PHAROS:  P02768 GTEx:  ENSG00000163631

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CPT	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	Cisplatin Cl2 H6 N2 Pt LXZZYRPGZAFOLE-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.16 Å
• R-Value Free:  0.329 (Depositor), 0.326 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.789	α = 90
b = 86.474	β = 103.7
c = 59.141	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-29 
Deposition Author(s): Merlino, A.

Revision History  

• Version 1.0: 2015-04-29
  Type: Initial release
  
• Version 1.1: 2015-06-17
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary