7Z57

Crystal structure of Human Serum Albumin in complex with surfactant GenX (2,3,3,3-tetrafluoro-2-(heptafluoropropoxy) propanoate)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.237 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Investigation of the Interaction between Human Serum Albumin and Branched Short-Chain Perfluoroalkyl Compounds.

Moro, G.Liberi, S.Vascon, F.Linciano, S.De Felice, S.Fasolato, S.Foresta, C.De Toni, L.Di Nisio, A.Cendron, L.Angelini, A.

(2022) Chem Res Toxicol 35: 2049-2058

  • DOI: https://doi.org/10.1021/acs.chemrestox.2c00211
  • Primary Citation of Related Structures:  
    7Z57

  • PubMed Abstract: 

    The current trend dealing with the production of per- and polyfluoroalkyl substances (PFASs) involves the shifting toward branched short-chain fluorinated compounds known as new-generation PFASs. A key aspect to be clarified, to address the adverse health effects associated with the exposure to PFASs, is their binding mode to human serum albumin (hSA), the most abundant protein in plasma. In this study, we investigated the interaction between hSA and two representative branched short-chain PFASs, namely, HPFO-DA and C6O4. In-solution studies revealed that both compounds bind hSA with affinities and stoichiometries lower than that of the legacy long-chain perfluoroalkyl compound PFOA. Competition experiments using hSA-binding drugs with known site-selectivity revealed that both HPFO-DA and C6O4 bound to pockets located in subdomain IIIA. The crystal structure of hSA in complex with HPFO-DA unveiled the presence of two binding sites. The characterization and direct comparison of hSA interactions with new-generation PFASs may be key elements for the understanding of the toxicological impact of these compounds.


  • Organizational Affiliation

    Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Venice, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Albumin584Homo sapiensMutation(s): 0 
Gene Names: ALBGIG20GIG42PRO0903PRO1708PRO2044PRO2619PRO2675UNQ696/PRO1341
UniProt & NIH Common Fund Data Resources
Find proteins for P02768 (Homo sapiens)
Explore P02768 
Go to UniProtKB:  P02768
PHAROS:  P02768
GTEx:  ENSG00000163631 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02768
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IGB (Subject of Investigation/LOI)
Query on IGB

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
(2R)-2,3,3,3-tetrakis(fluoranyl)-2-[1,1,2,2,3,3,3-heptakis(fluoranyl)propoxy]propanoic acid
C6 H F11 O3
CSEBNABAWMZWIF-REOHCLBHSA-N
MYR
Query on MYR

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
K [auth A]
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
D [auth A]
H [auth A]
I [auth A]
J [auth A]
L [auth A]
D [auth A],
H [auth A],
I [auth A],
J [auth A],
L [auth A],
M [auth A]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
BR
Query on BR

Download Ideal Coordinates CCD File 
N [auth A]BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.237 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 185.89α = 90
b = 38.769β = 105
c = 96.446γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministero dell Universita e della RicercaItaly--

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-12
    Type: Initial release
  • Version 1.1: 2022-11-30
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description