2VDB

Structure of human serum albumin with S-naproxen and the GA module


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 

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Literature

Structural Basis for the Binding of Naproxen to Human Serum Albumin in the Presence of Fatty Acids and the Ga Module.

Lejon, S.Cramer, J.F.Nordberg, P.A.

(2008) Acta Crystallogr Sect F Struct Biol Cryst Commun 64: 64

  • DOI: 10.1107/S174430910706770X
  • Primary Citation of Related Structures:  
    2VDB

  • PubMed Abstract: 
  • The previously determined crystal structure of the bacterial albumin-binding GA module in complex with human serum albumin (HSA) suggested the possibility of utilizing the complex in the study of ligand binding to HSA. As a continuation of these studies, the crystal structure of the HSA-GA complex with the drug molecule naproxen and the fatty acid decanoate bound to HSA has been determined to a resolution of 2 ...

    The previously determined crystal structure of the bacterial albumin-binding GA module in complex with human serum albumin (HSA) suggested the possibility of utilizing the complex in the study of ligand binding to HSA. As a continuation of these studies, the crystal structure of the HSA-GA complex with the drug molecule naproxen and the fatty acid decanoate bound to HSA has been determined to a resolution of 2.5 A. In terms of drug binding, the structure suggests that the binding of decanoate to the albumin molecule may play a role in making the haemin site in subdomain IB of the albumin molecule available for the binding of naproxen. In addition, structure comparisons with solved structures of HSA and of the HSA-GA complex show that the GA module is capable of binding to different conformations of HSA. The HSA-GA complex therefore emerges as a possible platform for the crystallographic study of specific HSA-drug interactions and of the influence exerted by the presence of fatty acids.


    Organizational Affiliation

    Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, S-751 24 Uppsala, Sweden. sara@xray.bmc.uu.se



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SERUM ALBUMINA579Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02768
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PEPTOSTREPTOCOCCAL ALBUMIN-BINDING PROTEINB55Finegoldia magnaMutation(s): 0 
Gene Names: pab
UniProt
Find proteins for Q51911 (Finegoldia magna)
Explore Q51911 
Go to UniProtKB:  Q51911
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ51911
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NPS
Query on NPS

Download Ideal Coordinates CCD File 
I [auth A](2S)-2-(6-methoxynaphthalen-2-yl)propanoic acid
C14 H14 O3
CMWTZPSULFXXJA-VIFPVBQESA-N
 Ligand Interaction
DKA
Query on DKA

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
DECANOIC ACID
C10 H20 O2
GHVNFZFCNZKVNT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 190.507α = 90
b = 49.462β = 93
c = 79.933γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-02-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance