3JQZ

Crystal Structure of Human serum albumin complexed with Lidocaine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Crystallographic analysis reveals a unique lidocaine binding site on human serum albumin.

Hein, K.L., Kragh-Hansen, U., Morth, J.P., Jeppesen, M.D., Otzen, D., Moller, J.V., Nissen, P.

(2010) J Struct Biol 

  • DOI: 10.1016/j.jsb.2010.03.014
  • Primary Citation of Related Structures:  
    3JRY, 3JQZ

  • PubMed Abstract: 

    • Human serum albumin (HSA), the major protein component in blood plasma and in extravascular spaces, is known to participate in the binding and transport of a variety of endogenous and exogenous organic compounds with anionic or electronegative featur ...

    Human serum albumin (HSA), the major protein component in blood plasma and in extravascular spaces, is known to participate in the binding and transport of a variety of endogenous and exogenous organic compounds with anionic or electronegative features. We here report on the 3.3A resolution crystal structure of HSA complexed with the cationic, and widely used, anesthetic lidocaine. We find that lidocaine and HSA co-crystallise as a dimer in the unusual space group I4(1). The dimer consists of one HSA molecule without ligand and one HSA molecule with a single, bound lidocaine. HSA is a heart-shaped protein composed of three homologous helical domains (I-III), which can be subdivided into two subdomains (A and B), and lidocaine binds to a unique site formed by residues from subdomain IB facing the central, interdomain crevice. In the crystal, binding seems to introduce only local conformational changes in the protein. According to intrinsic fluorescence experiments with aqueous HSA binding results in widespread conformational changes involving Trp214 in subdomain IIA. Results obtained with equilibrium dialysis and isothermal titration calorimetry show that lidocaine binding is of a low affinity and occurs at one discrete binding site in accordance with the X-ray data. Another crystal form of ligand-free HSA obtained in the presence of ammonium sulphate was determined at 2.3A resolution revealing a sulphate ion accepting cavity at the surface of subdomain IIIA. The present results contribute to a further characterisation of the exceptional binding properties of HSA.

    Organizational Affiliation: 

    Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10C, DK-8000 Arhus C, Denmark.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serum albuminA, B585Homo sapiensMutation(s): 0 
Gene Names: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341
Find proteins for P02768 (Homo sapiens)
Explore P02768 
Go to UniProtKB:  P02768
NIH Common Fund Data Resources
PHAROS  P02768
GTEx  ENSG00000163631
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LQZ
Query on LQZ
Download Ideal Coordinates CCD File 
A
2-(diethylamino)-N-(2,6-dimethylphenyl)ethanamide
C14 H22 N2 O
NNJVILVZKWQKPM-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 168.476α = 90
b = 168.476β = 90
c = 97.02γ = 90
Software Package:
Software NamePurpose
RemDAqdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-04-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description