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(-) Description

Title :  CRYSTAL STRUCTURE OF MICHAELIS SERPIN-TRYPSIN COMPLEX
 
Authors :  S. Ye, A. L. Cech, R. Belmares, R. C. Bergstrom, Y. Tong, D. R. Corey, M. R. Kanost, E. J. Goldsmith
Date :  29 Oct 01  (Deposition) - 21 Nov 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  E,I
Keywords :  Michaelis Serpin-Protease Complex Inhibitory Triad, Hydrolase/Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Ye, A. L. Cech, R. Belmares, R. C. Bergstrom, Y. Tong, D. R. Corey, M. R. Kanost, E. J. Goldsmith
The Structure Of A Michaelis Serpin-Protease Complex.
Nat. Struct. Biol. V. 8 979 2001
PubMed-ID: 11685246  |  Reference-DOI: 10.1038/NSB1101-979
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALASERPIN
    ChainsI
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidH6PQE-60
    Expression System StrainXL1-BLUE
    Expression System Taxid562
    Expression System Vector TypePLASMID
    MutationYES
    Organism CommonTOBACCO HORNWORM
    Organism ScientificMANDUCA SEXTA
    Organism Taxid7130
    SynonymSERPIN 1
 
Molecule 2 - TRYPSIN II ANIONIC
    ChainsE
    EC Number3.4.21.4
    EngineeredYES
    Expression SystemSACCHAROMYCES CEREVISIAE
    Expression System CommonBAKER'S YEAST
    Expression System PlasmidPYT
    Expression System Taxid4932
    Expression System Vector TypePLASMID
    MutationYES
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymPRETRYPSINOGEN II

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit EI

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1K9O)

(-) Sites  (0, 0)

(no "Site" information available for 1K9O)

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1E:22 -E:157
2E:42 -E:58
3E:128 -E:232
4E:136 -E:201
5E:168 -E:182
6E:191 -E:220

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1K9O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1K9O)

(-) PROSITE Motifs  (4, 4)

Asymmetric/Biological Unit (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.TRY2_RAT24-244  1E:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.TRY2_RAT59-64  1E:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.TRY2_RAT194-205  1E:189-200
4SERPINPS00284 Serpins signature.SERA_MANSE367-377  1I:361-371

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000188521ENSRNOE00000331572chr4:69088288-6908832740TRY2_RAT1-14140--
1.2bENSRNOT000000188522bENSRNOE00000277233chr4:69090744-69090903160TRY2_RAT14-67541E:16-61 (gaps)46
1.3ENSRNOT000000188523ENSRNOE00000105498chr4:69092114-69092367254TRY2_RAT67-152861E:61-149 (gaps)89
1.4ENSRNOT000000188524ENSRNOE00000338303chr4:69092772-69092908137TRY2_RAT152-197461E:149-192 (gaps)50
1.5ENSRNOT000000188525ENSRNOE00000134316chr4:69093163-69093367205TRY2_RAT198-246491E:193-245 (gaps)56

(-) 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 E from PDB  Type:PROTEIN  Length:223
 aligned with TRY2_RAT | P00763 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:223
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243   
            TRY2_RAT     24 IVGGYTCQENSVPYQVSLNSGYHFCGGSLINDQWVVSAAHCYKSRIQVRLGEHNINVLEGNEQFVNAAKIIKHPNFDRKTLNNDIMLIKLSSPVKLNARVATVALPSSCAPAGTQCLISGWGNTLSSGVNEPDLLQCLDAPLLPQADCEASYPGKITDNMVCVGFLEGGKDSCQGDSGGPVVCNGELQGIVSWGYGCALPDNPGVYTKVCNYVDWIQDTIAAN  246
               SCOP domains d1k9oe_ E: Trypsin(ogen)                                                                                                                                                                                                        SCOP domains
               CATH domains 1k9oE01     1k9oE02 E:28-120,E:233-245 Trypsin-like serine proteases                                  1k9oE01 E:16-27,E:121-232 Trypsin-like serine proteases                                                     1k9oE02       CATH domains
               Pfam domains Trypsin-1k9oE01 E:16-238                                                                                                                                                                                                ------- Pfam domains
         Sec.struct. author ....ee........eeeee...eeeeeeeee..eeeehhhhh....eeee............eeeeeeeeee.............eeeee........................eeeeee...............eeeeee..hhhhhhhhh.......eeee................eeee..eeeeeeeee.........eeeee...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: E:16-243 UniProt: 24-244                                                                                                                                                                                   -- PROSITE (1)
                PROSITE (2) -----------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ----------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2b  PDB: E:16-61 (gaps) [INCOMPLETE] ------------------------------------------------------------------------------------Exon 1.4  PDB: E:149-192 (gaps)               Exon 1.5  PDB: E:193-245 (gaps) UniProt: 198-246  Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.3  PDB: E:61-149 (gaps) UniProt: 67-152                                        ---------------------------------------------------------------------------------------------- Transcript 1 (2)
                1k9o E   16 IVGGYTCQENSVPYQVSLNSGYHFCGGSLINDQWVVSAAHCYKSRIQVRLGEHNINVLEGNEQFVNAAKIIKHPNFDRKTLNNDIMLIKLSSPVKLNARVATVALPSSCAPAGTQCLISGWGNTLSSGVNEPDLLQCLDAPLLPQADCEASYPGKITDNMVCVGFLEGGKDSCQGDAGGPVVCNGELQGIVSWGYGCALPDNPGVYTKVCNYVDWIQDTIAAN  245
                                    25        37        47        57        67|       78        88        98       108       118      |129||     140       150       160       170       180   |||1188|      198     ||212    || 222       232       242   
                                             34|                            67|                                                     125|  ||                                                 184||  |||            204|     217| |||                       
                                              37                             69                                                      127  ||                                                 1184|  |||             209      219 |||                       
                                                                                                                                        130|                                                   185  |||                        221||                       
                                                                                                                                         132                                                      188||                        1221|                       
                                                                                                                                                                                                  1188|                          222                       
                                                                                                                                                                                                    189                                                    

Chain I from PDB  Type:PROTEIN  Length:376
 aligned with SERA_MANSE | P14754 from UniProtKB/Swiss-Prot  Length:392

    Alignment length:376
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386      
          SERA_MANSE     17 GETDLQKILRESNDQFTAQMFSEVVKANPGQNVVLSAFSVLPPLGQLALASVGESHDELLRALALPNDNVTKDVFADLNRGVRAVKGVDLKMASKIYVAKGLELNDDFAAVSRDVFGSEVQNVDFVKSVEAAGAINKWVEDQTNNRIKNLVDPDALDETTRSVLVNAIYFKGSWKDKFVKERTMDRDFHVSKDKTIKVPTMIGKKDVRYADVPELDAKMIEMSYEGDQASMIIILPNQVDGITALEQKLKDPKALSRAEERLYNTEVEIYLPKFKIETTTDLKEVLSNMNIKKLFTPGAARLENLLKTKESLYVDAAIQKAFIEVNEEGAEAAAANAFGIVPASLILYPEVHIDRPFYFELKIDGIPMFNGKVIEP  392
               SCOP domains d1k9oi_ I: Alaserpin (serpin 1)                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1k9oI01 I:11-179,I:287-332 Antithrombin, subunit I, domain 2                                                                                                             1k9oI02 I:180-286,I:333-386 Alpha-1-antitrypsin, domain 1                                                  1k9oI01 I:11-179,I:287-332                    1k9oI02 I:180-286,I:333-386                            CATH domains
               Pfam domains ----------Serpin-1k9oI01 I:21-386                                                                                                                                                                                                                                                                                                                                                        Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh......eee.hhhhhhhhhhhh....hhhhhhhhhhh.....hhhhhhhhhhh...........eeeeeeeee......hhhhh.........eeee...hhhhhhhhhhhhhhhhh........hhhhh.....eeeeeeeeee.......hhhhheeeee.......eeeeeeeeeeeeeeeee....eeeeeee.hhh.eeeeeeee....hhhhhhhhh.............eeeeeeeeee.eeeeeeeehhhhhhh...........................eeeeeeeeee...............ee.......eee....eeeeeee...eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SERPIN     --------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1k9o I   11 GETDLQKILRESNDQFTAQMFSEVVKANPGQNVVLSAFSVLPPLGQLALASVGESHDELLRALALPNDNVTKDVFADLNRGVRAVKGVDLKMASKIYVAKGLELNDDFAAVSRDVFGSEVQNVDFVKSVEAAGAINKWVEDQTNNRIKNLVDPDALDETTRSVLVNAIYFKGSWKDKFVKERTMDRDFHVSKDKTIKVPTMIGKKDVRYADVPELDAKMIEMSYEGDQASMIIILPNQVDGITALEQKLKDPKALSRAEERLYNTEVEITLPKFKIETTTDLKEVLSNMNIKKLFTPGAARLENLLKTKESLTVDAAIQKAFIEVNEEGAEAAAANAFGIVPKSLILYPEVHIDRPFYFELKIDGIPMFNGKVIEP  386
                                    20        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      

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (3, 4)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (18, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain E   (TRY2_RAT | P00763)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    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:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0030574    collagen catabolic process    The proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix, usually carried out by proteases secreted by nearby cells.
    GO:0007586    digestion    The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0007584    response to nutrient    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nutrient stimulus.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    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.

Chain I   (SERA_MANSE | P14754)
molecular function
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
    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: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.
cellular component
    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.

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  TRY2_RAT | P00763
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 Related Entries

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

UniProtKB/Swiss-Prot
        SERA_MANSE | P147541sek
        TRY2_RAT | P007631amh 1anb 1anc 1and 1ane 1bra 1brb 1brc 1co7 1dpo 1ezs 1ezu 1f5r 1f7z 1fy8 1j14 1j15 1j16 1j17 1ql9 1slu 1slv 1slw 1slx 1trm 1ykt 1ylc 1yld 2trm 3fp6 3fp7 3fp8 3tgi 3tgj 3tgk

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1K9O)