Show PDB file:   
         Plain Text   HTML   (compressed file size)
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Authors :  S. -E. Ryu, H. -J. Choi
Date :  11 May 97  (Deposition) - 20 Aug 97  (Release) - 24 Feb 09  (Revision)
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Serine Protease Inhibitor, Alpha-1-Antitrypsin, Conformational Transition, Loop Flexibility, Metastability, Stabilizing Mutations (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  S. E. Ryu, H. J. Choi, K. S. Kwon, K. N. Lee, M. H. Yu
The Native Strains In The Hydrophobic Core And Flexible Reactive Loop Of A Serine Protease Inhibitor: Crystal Structure Of An Uncleaved Alpha1-Antitrypsin At 2. 7 A.
Structure V. 4 1181 1996
PubMed-ID: 8939743  |  Reference-DOI: 10.1016/S0969-2126(96)00126-8
(for further references see the PDB file header)

(-) Compounds

    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1ATU)

(-) Sites  (0, 0)

(no "Site" information available for 1ATU)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ATU)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1ATU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (32, 32)

Asymmetric/Biological Unit (32, 32)
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
08UniProtVAR_006988T92IA1AT_HUMANUnclassified  ---AA68I
10UniProtVAR_006989P112TA1AT_HUMANUnclassified  ---AP88T
16UniProtVAR_006995Q180EA1AT_HUMANUnclassified  ---AQ156E
27UniProtVAR_007006P386HA1AT_HUMANUnclassified  ---AP362H
32UniProtVAR_007011P415HA1AT_HUMANUnclassified  ---AP391H

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
1SERPINPS00284 Serpins signature.A1AT_HUMAN388-398  1A:364-373

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength

(-) 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:374
 aligned with A1AT_HUMAN | P01009 from UniProtKB/Swiss-Prot  Length:418

    Alignment length:374
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414    
               SCOP domains d1atua_ A: Antitrypsin, alpha-1                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains --1atuA02 A:23-194,A:290-358 Antithrombin, subunit I, domain 2                                                                                                                1atuA01 A:195-289 Alpha-1-antitrypsin, domain 1                                                1atuA02 A:23-194,A:290-358 Antithrombin, subunit I, domain 2         ------------------------------------ CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) hhhhhhhhhhhhhhhhhhhhhhhhh...----hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh....eeeeeeeeeee.......hhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhhhh...............eeeeeeeeeeee........eeeeee.......eeeeeeeeee...eeeeee....eeeeeeee..eeeeeeee....hhhhhhhhhhhhhhhh.........eeeee.eeeeeeeeehhhhhhhh......................eeeeeeeeeeeee...................eeeeeee.eeeeeeee.eeeeeeeeeee..... Sec.struct. author (1)
     Sec.struct. author (2) ----------------------------eeeee----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
             SAPs(SNPs) (1) -------------T----C-P---F-------F------T------EI----------------M--T---N--------H-------------S--------------------------------R-------E-----------------------------------------------K--------A---------C--------------------------------V-------V-----------------------------------------------------------------F-----T----NK---------------R---HK-----L------D--------------H--- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------------------------------------------------------------------------------------------W---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T-------------------------------- SAPs(SNPs) (2)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SERPIN     -------------------- PROSITE
           Transcript 1 (1) Exon 1.3b  PDB: A:21-192 UniProt: 1-216 [INCOMPLETE]                                                                                                                        -----------------------------------------------------------------------------------------Exon 1.5a  PDB: A:282-331 UniProt: 306-355        Exon 1.6b  PDB: A:332-394 UniProt: 356-418                      Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.4a  PDB: A:192-282 UniProt: 216-306                                                 ---------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390    

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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

(-) 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 1ATU)

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (A1AT_HUMAN | P01009)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
    GO:0002020    protease binding    Interacting selectively and non-covalently with any protease or peptidase.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004867    serine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
    GO:0048208    COPII vesicle coating    The addition of COPII proteins and adaptor proteins to ER membranes during the formation of transport vesicles, forming a vesicle coat.
    GO:0006888    ER to Golgi vesicle-mediated transport    The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
    GO:0006953    acute-phase response    An acute inflammatory response that involves non-antibody proteins whose concentrations in the plasma increase in response to infection or injury of homeothermic animals.
    GO:0007596    blood coagulation    The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
    GO:0007599    hemostasis    The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
    GO:0010951    negative regulation of endopeptidase activity    Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
    GO:0010466    negative regulation of peptidase activity    Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
    GO:0002576    platelet degranulation    The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
cellular component
    GO:0030134    COPII-coated ER to Golgi transport vesicle    A vesicle with a coat formed of the COPII coat complex proteins. The COPII coat complex is formed by the Sec23p/Sec24p and the Sec13p/Sec31p heterodimers. COPII-associated vesicles transport proteins from the rough endoplasmic reticulum to the Golgi apparatus (anterograde transport).
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.
    GO:0033116    endoplasmic reticulum-Golgi intermediate compartment membrane    The lipid bilayer surrounding any of the compartments of the endoplasmic reticulum (ER)-Golgi intermediate compartment system.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0031093    platelet alpha granule lumen    The volume enclosed by the membrane of the platelet alpha granule.
    GO:0005578    proteinaceous extracellular matrix    A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.


(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1atu)
(no "Sites" information available for 1atu)
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1atu)

(-) Still Images

  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
Access by UniProt ID/Accession number
  A1AT_HUMAN | P01009
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
Access by UniProt ID/Accession number
  A1AT_HUMAN | P01009
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

        A1AT_HUMAN | P010091d5s 1ezx 1hp7 1iz2 1kct 1oo8 1oph 1psi 1qlp 1qmb 2d26 2qug 3cwl 3cwm 3drm 3dru 3ndd 3ndf 3ne4 3t1p 4pyw 5io1 7api 8api 9api

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1ATU)