3KQ0

Crystal structure of human alpha1-acid glycoprotein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

wwPDB Validation 3D Report Full Report



Literature

The 1.8-A crystal structure of alpha1-acid glycoprotein (Orosomucoid) solved by UV RIP reveals the broad drug-binding activity of this human plasma lipocalin.

Schonfeld, D.L.Ravelli, R.B.Mueller, U.Skerra, A.

(2008) J Mol Biol 384: 393-405

  • DOI: 10.1016/j.jmb.2008.09.020
  • Primary Citation of Related Structures:  
    3KQ0

  • PubMed Abstract: 
  • Alpha(1)-acid glycoprotein (AGP) is an important drug-binding protein in human plasma and, as an acute-phase protein, it has a strong influence on pharmacokinetics and pharmacodynamics of many pharmaceuticals. We report the crystal structure of the r ...

    Alpha(1)-acid glycoprotein (AGP) is an important drug-binding protein in human plasma and, as an acute-phase protein, it has a strong influence on pharmacokinetics and pharmacodynamics of many pharmaceuticals. We report the crystal structure of the recombinant unglycosylated human AGP at 1.8 A resolution, which was solved using the new method of UV-radiation-damage-induced phasing (UV RIP). AGP reveals a typical lipocalin fold comprising an eight-stranded beta-barrel. Of the four loops that form the entrance to the ligand-binding site, loop 1, which connects beta-strands A and B, is among the longest observed so far and exhibits two full turns of an alpha-helix. Furthermore, it carries one of the five N-linked glycosylation sites, while a second one occurs underneath the tip of loop 2. The branched, partly hydrophobic, and partly acidic cavity, together with the presumably flexible loop 1 and the two sugar side chains at its entrance, explains the diverse ligand spectrum of AGP, which is known to vary with changes in glycosylation pattern.


    Organizational Affiliation

    Lehrstuhl für Biologische Chemie, Technische Universität München, An der Saatzucht 5, 85350 Freising-Weihenstephan, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alpha-1-acid glycoprotein 1A192Homo sapiensMutation(s): 0 
Gene Names: AGP-AAGP1ORMORM1
Find proteins for P02763 (Homo sapiens)
Explore P02763 
Go to UniProtKB:  P02763
NIH Common Fund Data Resources
PHAROS  P02763
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JIM
Query on JIM

Download CCD File 
A
(2R)-2,3-dihydroxypropyl acetate
C5 H10 O4
KMZHZAAOEWVPSE-RXMQYKEDSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
AL-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.894α = 90
b = 78.894β = 90
c = 93.384γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
SHELXDphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2019-12-25
    Changes: Advisory, Database references, Derived calculations, Polymer sequence