Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
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

Title :  THE X-RAY CRYSTAL STRUCTURE OF A SERPIN FROM A THERMOPHILIC PROKARYOTE
 
Authors :  J. A. Irving, L. D. Cabrita, J. Rossjohn, R. N. Pike, S. P. Bottomley, J. C. Whisstock
Date :  21 Sep 02  (Deposition) - 15 Apr 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Protease Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. A. Irving, L. D. Cabrita, J. Rossjohn, R. N. Pike, S. P. Bottomley, J. C. Whisstock
The 1. 5 A Crystal Structure Of A Prokaryote Serpin: Controlling Conformational Change In A Heated Environment
Structure V. 11 387 2003
PubMed-ID: 12679017  |  Reference-DOI: 10.1016/S0969-2126(03)00057-1
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SERINE PROTEINASE INHIBITOR (SERPIN), CHAIN A
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentCHAIN A, RESIDUE 55-377
    Organism ScientificTHERMOBIFIDA FUSCA
    Organism Taxid2021
 
Molecule 2 - SERINE PROTEINASE INHIBITOR (SERPIN), CHAIN B
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentCHAIN B, RESIDUE 378-420
    Organism ScientificTHERMOBIFIDA FUSCA
    Organism Taxid2021

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1MTP)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1MTP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1MTP)

(-) Exons   (0, 0)

(no "Exon" information available for 1MTP)

(-) 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:320
 aligned with Q47NK3_THEFY | Q47NK3 from UniProtKB/TrEMBL  Length:366

    Alignment length:320
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322
         Q47NK3_THEFY     3 GGFLRDDHLEFALHLHRRLAEAVPDGEVIWSPYSVACALGVLAAGARATTRTELTTLLGTDPAPLLAALDRAVADSPDLASRTVLWVSADVPVRSSFRATVHDRPDSDVRTADFRTNPEGVRATVNADIADATRGMIRELLPQGAVTPDLRAILTNALWARARWTTPFEAHLTREGTFRTPRGPKRVPFMHRTGTMPYATARGWGMVTLHAHDELAVDVLLPPGTNAAAVPTAPLLTALHRRSASTSVELALPRFELTQPHQLVEVLAEAGVRTLFTASADLSGISTVPLYVDTVIHQARLRVDERGAEGAAATAAMMLL 322
               SCOP domains d1mtp.1 A:,B: Thermopin                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1mtpA01 A:5-167,A:259-323 Antithrombin, subunit I, domain 2                                                                                                        1mtpA02 A:168-258 Alpha-1-antitrypsin, domain 1                                            1mtpA01 A:5-167,A:259-323 Antithrombin, subunit I, domain 2      - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhh.....eeeeeeeee......hhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhh................eeeeeeeeeeeeee.....hhhhheeeeeee..eeeeeeeeeeeeeeeeeee..eeeeeee....eeeeeee.hhhhh....hhhhhhhhhhhheeeeeeeeee.eeeeeeeehhhhhhhh..hhhhh.............eeeeeeeeeeeeee..eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mtp A   5 GGFLRDDHLEFALHLHRRLAEAVPDGEVIWSPYSVACALGVLAAGARATTRTELTTLLGTDPAPLLAALDRAVTDSPDLASRTVLWVSADVPVRSSFRATMHDRPDSDVRTADFRTNPEGVRATVNADIADATRGMIRELLPQGAVTPDLRAILTNALWAKARWTTPFEAHLTREGTFRTPRGPKRVPFMHRTKTMPYATARGWRMVTLHAHDELAVDVLLPPGTNAAAVPTAPLLTALHRRSASTSVELALPRFELTQPHQLVEVLAEAGVRTLFTASADLSGISTVPLYVDTVIHQARLRVDERGAEGAAATAAMMLL 324
                                    14        24        34        44        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

Chain B from PDB  Type:PROTEIN  Length:35
 aligned with Q47NK3_THEFY | Q47NK3 from UniProtKB/TrEMBL  Length:366

    Alignment length:35
                                   340       350       360     
         Q47NK3_THEFY   331 TIRFSVDRPFHIVVRRRGAILFLGSIADPHDPGPA 365
               SCOP domains d1mtp.1 A:,B: Thermopin             SCOP domains
               CATH domains ----------------------------------- CATH domains
           Pfam domains (1) Serpin-1mtpB01 B:333-361     ------ Pfam domains (1)
           Pfam domains (2) Serpin-1mtpB02 B:333-361     ------ Pfam domains (2)
         Sec.struct. author .eeee....eeeeeee..eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------- PROSITE
                 Transcript ----------------------------------- Transcript
                 1mtp B 333 TIRFSVDRPFHIVVRRRGAILFLGSIADPHDPGPA 367
                                   342       352       362     

   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  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q47NK3_THEFY | Q47NK3)
cellular component
    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.

 Visualization

(-) 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)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(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 1mtp)
 
  Sites
(no "Sites" information available for 1mtp)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1mtp)
 

(-) Still Images

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

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1mtp
    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
  Q47NK3_THEFY | Q47NK3
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  Q47NK3_THEFY | Q47NK3
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q47NK3_THEFY | Q47NK31sng

(-) Related Entries Specified in the PDB File

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