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

(-) Description

Title :  STRUCTURE OF PORCINE TRYPSIN COMPLEXED WITH BDELLASTASIN, AN ANTISTASIN-TYPE INHIBITOR
 
Authors :  U. Rester, M. Moser, R. Huber, W. Bode
Date :  02 Mar 00  (Deposition) - 02 Mar 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Complex (Hydrolase/Inhibitor), Hydrolase, Inhibitor, Bdellastasin, Antistasin, Trypsin (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  U. Rester, M. Moser, R. Huber, W. Bode
L-Isoaspartate 115 Of Porcine Beta-Trypsin Promotes Crystallization Of Its Complex With Bdellastasin.
Acta Crystallogr. , Sect. D V. 56 581 2000
PubMed-ID: 10771427  |  Reference-DOI: 10.1107/S0907444900003048
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRYPSIN
    ChainsA
    EC Number3.4.21.4
    Organism CommonPIG
    Organism ScientificSUS SCROFA
    Organism Taxid9823
    Other DetailsLYOPHILIZED PORCINE PANCREATIC B-TRYPSIN TYPEIX (E.C. 3.4.21.4) PURCHASED FROM SIGMA.
    TissuePANCREAS
 
Molecule 2 - BDELLASTASIN
    ChainsB
    EngineeredYES
    Expression SystemSACCHAROMYCES CEREVISIAE
    Expression System CommonBAKER'S YEAST
    Expression System StrainS78
    Expression System Taxid4932
    Expression System VectorPVT102U/ALPHA
    Organism CommonMEDICINAL LEECH
    Organism ScientificHIRUDO MEDICINALIS
    Organism Taxid6421

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:70 , ASN A:72 , VAL A:75 , GLU A:77 , GLU A:80BINDING SITE FOR RESIDUE NA A 246

(-) SS Bonds  (11, 11)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:157
2A:42 -A:58
3A:128 -A:232
4A:136 -A:201
5A:168 -A:182
6A:191 -A:220
7B:10 -B:21
8B:15 -B:26
9B:28 -B:48
10B:33 -B:52
11B:37 -B:54

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_TRYP_PIG_001 *I20VTRYP_PIG  ---  ---AI27V
   * ID not provided by source

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

(-) PROSITE Motifs  (4, 4)

Asymmetric/Biological Unit (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.TRYP_PIG9-229  1A:16-243
2ANTISTASINPS51252 Antistasin-like domain profile.BDEL_HIRME28-54  1B:28-54
3TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.TRYP_PIG44-49  1A:53-58
4TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.TRYP_PIG179-190  1A:189-200

(-) Exons   (0, 0)

(no "Exon" information available for 1EJA)

(-) 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: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 d1ejaa_ A: Trypsin(ogen)                                                                                                                                                                                                        SCOP domains
               CATH domains 1ejaA01     1ejaA02 A:28-120,A:233-245 Trypsin-like serine proteases                                  1ejaA01 A:16-27,A:121-232 Trypsin-like serine proteases                                                     1ejaA02       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeee...eeeeeeeee..eeeehhhhh....eeee............eeeeeeeeee.............eeeee........................eeeeee...............eeeeee..hhhhhhhhh.......eeee................eeee..eeeeeeeeee........eeeee...hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------V------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 9-229                                                                                                                                                                                    -- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ----------------------------------------- PROSITE (2)
                PROSITE (3) -----------------------------------TRYPSI-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1eja A   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 B from PDB  Type:PROTEIN  Length:53
 aligned with BDEL_HIRME | P82107 from UniProtKB/Swiss-Prot  Length:59

    Alignment length:53
                                    16        26        36        46        56   
          BDEL_HIRME      7 TTPCGPVTCSGAQMCEVDKCVCSDLHCKVKCEHGFKKDDNGCEYACICADAPQ   59
               SCOP domains d1ejab_ B: Bdellastasin                               SCOP domains
               CATH domains 1ejaB00 B:7-59 Antistasin; domain 1                   CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author .eee..eee....eee..eee...eee.......................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------ANTISTASIN  PDB: B:28-54   ----- PROSITE (2)
                 Transcript ----------------------------------------------------- Transcript
                1eja B    7 TTPCGPVTCSGAQMCEVDKCVCSDLHCKVKCEHGFKKDDNGCEYACICADAPQ   59
                                    16        26        36        46        56   

   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  (2, 3)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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 B   (BDEL_HIRME | P82107)
molecular function
    GO:0004857    enzyme inhibitor activity    Binds to and stops, prevents or reduces the activity of an enzyme.
    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
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1eja)
 

(-) 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
  1eja
    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
  BDEL_HIRME | P82107
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  TRYP_PIG | P00761
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.21.4
    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
  BDEL_HIRME | P82107
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  TRYP_PIG | P00761
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        BDEL_HIRME | P821071c9p 1c9t
        TRYP_PIG | P007611aks 1an1 1avw 1avx 1c9p 1d3o 1df2 1ept 1ewu 1fmg 1fn6 1fni 1h9h 1h9i 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

1c9p 1C9P CONTAINS THE SAME PROTEIN IN ANOTHER SPACEGROUP
1c9t 1C9T CONTAINS THE SAME INHIBITOR (BDELLASTASIN) COMPLEXED WITH BOVINE TRYPSIN