7API

THE S VARIANT OF HUMAN ALPHA1-ANTITRYPSIN, STRUCTURE AND IMPLICATIONS FOR FUNCTION AND METABOLISM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report



Literature

The S variant of human alpha 1-antitrypsin, structure and implications for function and metabolism.

Engh, R.Lobermann, H.Schneider, M.Wiegand, G.Huber, R.Laurell, C.B.

(1989) Protein Eng 2: 407-415

  • DOI: 10.1093/protein/2.6.407
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The S variant of the human alpha 1-antitrypsin with E-264----V, is responsible for a mild alpha 1-antitrypsin deficiency quite common in the European population. S protein specifically cleaved at the susceptible peptide bond was crystallized and its ...

    The S variant of the human alpha 1-antitrypsin with E-264----V, is responsible for a mild alpha 1-antitrypsin deficiency quite common in the European population. S protein specifically cleaved at the susceptible peptide bond was crystallized and its crystal structure determined and refined to 3.1 A resolution. The S variant crystallizes isomorphous to the normal M variant. The difference Fourier electron density map shows the E----V change as outstanding residual density. In addition, small structural changes of the main polypeptide chain radiate from the site of mutation and affect parts far removed from it. By the mutation, internal hydrogen bonds and salt linkages of E-264 to Y-38 and K-487, respectively, are lost. They cause the far-reaching slight distortions and are probably related to the reduced thermal stability of the S mutant. They may also be responsible for slower folding of the polypeptide chain and the clinical symptoms of alpha 1-antitrypsin deficiency. In a theoretical study by molecular dynamics methods simulations of the M and S proteins were made and the results analysed with respect to structural and dynamic properties and compared with the experimental results. There is a significant correlation between experimental and theoretical results in some respects.


    Related Citations: 
    • Human Alpha1-Proteinase Inhibitor. Crystal Structure Analysis of Two Crystal Modifications, Molecular Model and Preliminary Analysis of the Implications for Function
      Loebermann, H., Tokuoka, R., Deisenhofer, J., Huber, R.
      (1984) J Mol Biol 177: 531
    • Interaction of Human Alpha1-Proteinase Inhibitor with Chymotrypsinogena and Crystallization of a Proteolytically Modified Alpha1-Proteinase Inhibitor
      Loebermann, H., Lottspeich, F., Bode, W., Huber, R.
      (1982) Hoppe Seylers Z Physiol Chem 363: 1377
    • The Biosynthesis of Rat Alpha1-Antitrypsin
      Carlson, J., Stenflo, J.
      (1982) J Biol Chem 257: 12987
    • Human Alpha1-Antitrypsin. Carbohydrate Attachment and Sequence Homology
      Carrell, R.W., Jeppsson, J.-O., Vaughan, L., Brennan, S.O., Owen, M.C., Boswell, D.R.
      (1981) FEBS Lett 135: 301
    • Studies on the Oligosaccharide Chains of Human Alpha1-Protease Inhibitor. II. Structure of Oligosaccharides
      Mega, T., Lujan, E., Yoshida, A.
      (1980) J Biol Chem 255: 4057

    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Martinsried, FRG.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALPHA 1-ANTITRYPSINA347Homo sapiensMutation(s): 0 
Gene Names: SERPINA1AATPIPRO0684PRO2209
Find proteins for P01009 (Homo sapiens)
Explore P01009 
Go to UniProtKB:  P01009
NIH Common Fund Data Resources
PHAROS  P01009
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ALPHA 1-ANTITRYPSINB36Homo sapiensMutation(s): 0 
Gene Names: SERPINA1AATPIPRO0684PRO2209
Find proteins for P01009 (Homo sapiens)
Explore P01009 
Go to UniProtKB:  P01009
NIH Common Fund Data Resources
PHAROS  P01009
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Oligosaccharides
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
6 N-Glycosylation
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D, E
2 N-Glycosylation
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CYS
Query on CYS

Download CCD File 
A
CYSTEINE
C3 H7 N O2 S
XUJNEKJLAYXESH-REOHCLBHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Work: 0.193 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.5α = 90
b = 120.5β = 90
c = 113.5γ = 90
Software Package:
Software NamePurpose
EREFrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1990-10-15
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary