Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 45.34 kDa 
• Atom Count: 3119 
• Residue Count: 375 
• Unique protein chains: 2

9API

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

• DOI: 10.2210/pdb9API/pdb

• Classification: PROTEINASE INHIBITOR
• Mutation(s): No 


• Deposited: 1988-09-08 Released: 1990-10-15 
• Deposition Author(s): Loebermann, H., Tokuoka, R., Deisenhofer, J., Huber, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Work: 0.209 

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

• PubMed: 2785270 
• 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 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
ALPHA 1-ANTITRYPSIN	A	347	N/A	Mutation(s): 0
Find proteins for P01009 (Homo sapiens) Explore P01009  Go to UniProtKB:  P01009
NIH Common Fund Data Resources
PHAROS  P01009 GTEx  ENSG00000197249

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
ALPHA 1-ANTITRYPSIN	B	36	N/A	Mutation(s): 0
Find proteins for P01009 (Homo sapiens) Explore P01009  Go to UniProtKB:  P01009
NIH Common Fund Data Resources
PHAROS  P01009 GTEx  ENSG00000197249

Oligosaccharides

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram
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

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E	2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CYS	A	CYSTEINE C3 H7 N O2 S XUJNEKJLAYXESH-REOHCLBHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Work: 0.209 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.3	α = 90
b = 119.3	β = 90
c = 104.3	γ = 90

Software Package:

Software Name	Purpose
EREF	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1988-09-08 
• Released Date: 1990-10-15 
Deposition Author(s): Loebermann, H., Tokuoka, R., Deisenhofer, J., Huber, R.

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