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(-) Description

Title :  THE S VARIANT OF HUMAN ALPHA1-ANTITRYPSIN, STRUCTURE AND IMPLICATIONS FOR FUNCTION AND METABOLISM
 
Authors :  H. Loebermann, R. Tokuoka, J. Deisenhofer, R. Huber
Date :  08 Sep 88  (Deposition) - 15 Oct 90  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Proteinase Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Engh, H. Lobermann, M. Schneider, G. Wiegand, R. Huber, C. B. Laurel
The S Variant Of Human Alpha 1-Antitrypsin, Structure And Implications For Function And Metabolism.
Protein Eng. V. 2 407 1989
PubMed-ID: 2785270  |  Reference-DOI: 10.1093/PROTEIN/2.6.407
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALPHA 1-ANTITRYPSIN
    Chains: A
    Engineered: YES
 
Molecule 2 - ALPHA 1-ANTITRYPSIN
    Chains: B
    Engineered: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1CYS1Mod. Amino AcidCYSTEINE
2MAN3Ligand/IonALPHA-D-MANNOSE
3NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:35 , ASN A:46 , LEU A:235 , PHE A:253 , HIS A:262 , LEU A:263 , GLU A:264 , ASN A:265 , GLU A:266 , LEU A:267 , ILE A:272 , NAG A:502 , LEU B:373BINDING SITE FOR RESIDUE NAG A 501
02AC2SOFTWAREPHE A:35 , LEU A:235 , LEU A:267 , ILE A:271 , ILE A:272 , PHE A:275 , NAG A:501 , MAN A:503BINDING SITE FOR RESIDUE NAG A 502
03AC3SOFTWAREASP A:270 , ILE A:271 , ILE A:272 , THR A:273 , LYS A:274 , PHE A:275 , CYS A:395 , NAG A:502 , MAN A:504 , MAN A:506BINDING SITE FOR RESIDUE MAN A 503
04AC4SOFTWAREASP A:270 , ILE A:271 , ILE A:272 , THR A:273 , LYS A:274 , PHE A:275 , LEU A:276 , GLU A:277 , MAN A:503 , NAG A:505BINDING SITE FOR RESIDUE MAN A 504
05AC5SOFTWARETHR A:273 , LEU A:276 , MAN A:504 , LYS B:380BINDING SITE FOR RESIDUE NAG A 505
06AC6SOFTWAREGLN A:212 , GLN A:230 , CYS A:232 , VAL A:239 , PHE A:275 , CYS A:395 , MAN A:503BINDING SITE FOR RESIDUE MAN A 506
07AC7SOFTWAREASN A:83 , THR A:85 , GLU A:86BINDING SITE FOR RESIDUE NAG A 510
08AC8SOFTWAREASP A:107 , ASN A:247 , NAG A:521 , ASN B:378BINDING SITE FOR RESIDUE NAG A 520
09AC9SOFTWARENAG A:520BINDING SITE FOR RESIDUE NAG A 521
10BC1SOFTWAREGLY A:148 , ASP A:149 , THR A:150 , GLN A:212 , CYS A:232 , LYS A:234 , MAN A:503 , MAN A:506BINDING SITE FOR RESIDUE CYS A 395

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:232 -A:395

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ile B:360 -Pro B:361

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 9API)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 9API)

(-) Exons   (0, 0)

(no "Exon" information available for 9API)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:339
                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d9api.1 A:,B: Antitrypsin, alpha-1                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ---9apiA02 A:23-194,A:290-358 Antithrombin, subunit I, domain 2                                                                                                                9apiA01 A:195-289 Alpha-1-antitrypsin, domain 1                                                9apiA02 A:23-194,A:290-358 Antithrombin, subunit I, domain 2          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) .hhhhhhhhhhhhhhhhhhhhhhhhh..-----hhhhhhhhhhhhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh....eeeeeeeeeeeee....hhhhhhhhhhhhh-------...hhhhhhhhhhhhhhhhh..............eeeeeeeeeeeee.....................eeeeeeeeeeee.eeeeee..eeeeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhhhh......------------------hhhhhhhh...................eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee Sec.struct. author (1)
     Sec.struct. author (2) ----------------------------eeeeeeee-----------------------------------------------------------------------------------eeeeeeee---------------------------------------------------------------------------------------------------------------------------------------eeeeeeeeeeeeeeeeeee---------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 9api A  20 HPTFNKITPNLAEFAFSLYRQLAHQSNSTNIFFSPVSIATAFAMLSLGTKADTHDEILEGLNFNLTEIPEAQIHEGFQELLRTLNQPDSQLQLTTGNGLFLSEGLKLVDKFLEDVKKLYHSEAFTVNFGDTEEAKKQINDYVEKGTQGKIVDLVKELDRDTVFALVNYIFFKGKWERPFEVKDTEEEDFHVDQVTTVKVPMMKRLGMFNIQHCKKLSSWVLLMKYLGNATAIFFLPDEGKLQHLENELTHDIITKFLENEDRRSASLHLPKLSITGTYDLKSVLGQLGITKVFSNGADLSGVTEEAPLKLSKAVHKAVLTIDEKGTEAAGAMFLEAIPM 358
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349         


Chain B from PDB  Type:PROTEIN  Length:36
                                                                    
               SCOP domains d9api.1 A:,B: Antitrypsin, alpha-1   SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee.eeeeeeeeeeeeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
                 Transcript ------------------------------------ Transcript
                 9api B 359 SIPPEVKFNKPFVFLMIEQNTKSPLFMGKVVNPTQK 394
                                   368       378       388
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 9API)

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)

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the following image was kindly provided by the protease and protease inhibitor web server prolysis.
  Alpha-1 Proteinase Inhibitor is an inhibitory member of the serpin superfamily in the cleaved conformation. Serpins share a common tertiary structure with three beta sheets and nine alpha helices. The inhibitory reactive site forms an exposed loop whith the P1-P1' residues acting as a bait for the target protease. The interaction with the protease leads to the formation of an irreversible serpin-enzyme complex, which is further cleaved at the P1-P1' peptide bond. After this cleavage, the central beta sheet (coloured white) undergo a considerable refolding since the P15-P1 region is incorporated in the central beta sheet where it forms a new strand (s4A coloured red here). In the cleaved conformation, the P1 residue (Met358) is separated from the P14 residue (Ser359) by 70Å (mono).
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        A1AT_HUMAN | P01009: 1atu 1d5s 1ezx 1hp7 1iz2 1kct 1oo8 1oph 1psi 1qlp 1qmb 2d26 2qug 3cwl 3cwm 3drm 3dru 3ndd 3ndf 3ne4 3t1p 4pyw 5io1 7api 8api

(-) Related Entries Specified in the PDB File

7api 8api