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

(-) Description

Title :  COMPLEX OF EETI-II MUTANT WITH PORCINE TRYPSIN
 
Authors :  R. Kraetzner, A. Wentzel, H. Kolmar, I. Uson
Date :  12 Mar 01  (Deposition) - 26 Jul 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  E,I
Keywords :  Hydrolase/Inhibitor, Complex (Serine Protease/Inhibitor), Trypsin, Squash Inhibitor, Cystine Knot (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Kraetzner, J. E. Debreczeni, T. Pape, T. R. Schneider, A. Wentzel, H. Kolmar, G. M. Sheldrick, I. Uson
Structure Of Ecballium Elaterium Trypsin Inhibitor Ii (Eeti-Ii): A Rigid Molecular Scaffold
Acta Crystallogr. , Sect. D V. 61 1255 2005
PubMed-ID: 16131759  |  Reference-DOI: 10.1107/S0907444905021207
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRYPSIN
    Chains: E
    EC Number: 3.4.21.4
    Organ: PANCREAS
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823
    Other Details: SIGMA
    Secretion: SALIVA
 
Molecule 2 - TRYPSIN INHIBITOR II
    Chains: I
    Engineered: YES
    Mutation: YES
    Organism Common: SQUIRTING CUCUMBER
    Organism Scientific: ECBALLIUM ELATERIUM
    Organism Taxid: 3679
    Other Details: C-TERMINAL TAG OF 6 HISTIDINES
    Synonym: EETI-II
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : EI

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU E:70 , ASN E:72 , VAL E:75 , GLU E:80 , HOH E:2031 , HOH E:2039BINDING SITE FOR RESIDUE CA E1246

(-) SS Bonds  (9, 9)

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
7I:2 -I:19
8I:9 -I:21
9I:15 -I:27

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1H9I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_TRYP_PIG_001 *I20VTRYP_PIG  ---  ---EI27V
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (4, 4)

Asymmetric/Biological Unit (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SQUASH_INHIBITORPS00286 Squash family of serine protease inhibitors signature.ITR2_ECBEL2-21  1I:2-21
2TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.TRYP_PIG9-229  1E:16-243
3TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.TRYP_PIG44-49  1E:53-58
4TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.TRYP_PIG179-190  1E:189-200

(-) Exons   (0, 0)

(no "Exon" information available for 1H9I)

(-) 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 TRYP_PIG | P00761 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:223
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228   
            TRYP_PIG      9 IVGGYTCAANSIPYQVSLNSGSHFCGGSLINSQWVVSAAHCYKSRIQVRLGEHNIDVLEGNEQFINAAKIITHPNFNGNTLDNDIMLIKLSSPATLNSRVATVSLPRSCAAAGTECLISGWGNTKSSGSSYPSLLQCLKAPVLSDSSCKSSYPGQITGNMICVGFLEGGKDSCQGDSGGPVVCNGQLQGIVSWGYGCAQKNKPGVYTKVCNYVNWIQQTIAAN  231
               SCOP domains d1h9ie_ E: Trypsin(ogen)                                                                                                                                                                                                        SCOP domains
               CATH domains 1h9iE01     1h9iE02 E:28-120,E:233-245 Trypsin-like serine proteases                                  1h9iE01 E:16-27,E:121-232 Trypsin-like serine proteases                                                     1h9iE02       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeee...eeeeeeeee..eeeehhhhh....eeee............eeeeeeeeee.............eeeee........................eeeeee...............eeeeee..hhhhhhhhh.......eeee................eeee..eeeeeeeee.........eeeee...hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------V------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) TRYPSIN_DOM  PDB: E:16-243 UniProt: 9-229                                                                                                                                                                                    -- PROSITE (2)
                PROSITE (1) -----------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ----------------------------------------- PROSITE (1)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1h9i E   16 IVGGYTCAANSIPYQVSLNSGSHFCGGSLINSQWVVSAAHCYKSRIQVRLGEHNIDVLEGNEQFINAAKIITHPNFNGNTLDNDIMLIKLSSPATLNSRVATVSLPRSCAAAGTECLISGWGNTKSSGSSYPSLLQCLKAPVLSDSSCKSSYPGQITGNMICVGFLEGGKDSCQGDSGGPVVCNGQLQGIVSWGYGCAQKNKPGVYTKVCNYVNWIQQTIAAN  245
                                    25        37        47        57        67|       78        88        98       108       118      |129||     140       150       160       170       180    | 188B       198     ||212    || 222       232       242   
                                             34|                            67|                                                     125|  ||                                                 184B 188B             204|     217|  |                        
                                              37                             69                                                      127  ||                                                                        209      219  |                        
                                                                                                                                        130|                                                                                   221B                        
                                                                                                                                         132                                                                                                               


Chain I from PDB  Type:PROTEIN  Length:30
 aligned with ITR2_ECBEL | P12071 from UniProtKB/Swiss-Prot  Length:30

    Alignment length:30
                                    10        20        30
          ITR2_ECBEL      1 GCPRILMRCKQDSDCLAGCVCGPNGFCGSP   30
               SCOP domains d1h9ii_ I: Trypsin inhibitor   SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author .ee.......hhhhh....ee.....ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE -SQUASH_INHIBITOR    --------- PROSITE
                 Transcript ------------------------------ Transcript
                1h9i I    1 GCPRILIRCKQDSDCLAGCVCTNNKFCGSP   30
                                    10        20        30
   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
(-)
Class: All beta proteins (24004)
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1H9I)

(-) Gene Ontology  (14, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain E   (TRYP_PIG | P00761)
molecular function
    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: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: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.
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.

Chain I   (ITR2_ECBEL | P12071)
molecular function
    GO:0004866    endopeptidase inhibitor activity    Stops, prevents or reduces the activity of an endopeptidase, any enzyme that hydrolyzes nonterminal peptide bonds in polypeptides.
    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.

 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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1h9i)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1h9i
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  ITR2_ECBEL | P12071
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  TRYP_PIG | P00761
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.21.4
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  ITR2_ECBEL | P12071
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  TRYP_PIG | P00761
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        ITR2_ECBEL | P12071: 1h9h 1w7z 2c4b 2eti 2it7 2let
        TRYP_PIG | P00761: 1aks 1an1 1avw 1avx 1c9p 1d3o 1df2 1eja 1ept 1ewu 1fmg 1fn6 1fni 1h9h 1ldt 1lt2 1mct 1qqu 1s5s 1s6f 1s6h 1s81 1s82 1s83 1s84 1s85 1tfx 1tx6 1uhb 1v6d 1yf4 1z7k 2a31 2a32 3myw 4an7 4doq

(-) Related Entries Specified in the PDB File

1aks CRYSTAL STRUCTURE OF THE FIRST ACTIVE AUTOLYSATE FORM OF THE PORCINE ALPHA TRYPSIN
1an1 LEECH-DERIVED TRYPTASE INHIBITOR/TRYPSIN COMPLEX
1avw COMPLEX PORCINE PANCREATIC TRYPSIN/SOYBEAN TRYPSIN INHIBITOR, ORTHORHOMBIC CRYSTAL FORM
1avx COMPLEX PORCINE PANCREATIC TRYPSIN/SOYBEAN TRYPSIN INHIBITOR, TETRAGONAL CRYSTAL FORM
1c9p COMPLEX OF BDELLASTASIN WITH PORCINE TRYPSIN
1eja STRUCTURE OF PORCINE TRYPSIN COMPLEXED WITH BDELLASTASIN, AN ANTISTASIN-TYPE INHIBITOR
1ept PORCINE E-TRYPSIN
1ewu KNOWLEDGE BASED MODEL OF A SERINE PROTEASE INHIBITOR OFCUCURBITACEAE FAMILY (THEORETICAL MODEL) BOUND TO TRYPSIN.
1fmg CRYSTAL STRUCTURE OF PORCINE BETA TRYPSIN WITH 0.04%POLYDOCANOL
1fn6 CRYSTAL STRUCTURE OF PORCINE BETA TRYPSIN WITH 0.1%POLYDOCANOL
1fni CRYSTAL STRUCTURE OF PORCINE BETA TRYPSIN WITH 0.01%POLYDOCANOL
1h9h COMPLEX OF EETI-II WITH PORCINE TRYPSIN
1ldt COMPLEX OF LEECH-DERIVED TRYPTASE INHIBITOR WITH PORCINE TRYPSIN
1mct TRYPSIN COMPLEXED WITH INHIBITOR FROM BITTER GOURD
1qqu CRYSTAL STRUCTURE OF PORCINE BETA TRYPSIN WITH BOUND ACETATE ION
1tfx COMPLEX OF THE SECOND KUNITZ DOMAIN OF TISSUE FACTOR PATHWAY INHIBITOR WITH PORCINE TRYPSIN
2eti TRYPSIN INHIBITOR II (EETI II)
2let TRYPSIN INHIBITOR II MUTANT WITH ILE 5 REPLACED BY LEU (I5L) (NMR, 20 STRUCTURES)