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 :  ANIONIC TRYPSIN FROM PACIFIC CHUM SALMON
 
Authors :  E. Toyota, K. K. S. Ng, S. Kuninaga, H. Sekizaki, K. Itoh, K. Tanizawa, M. N. G. James
Date :  03 Aug 02  (Deposition) - 11 Dec 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Psychrophilic Enzymes, Proteinase-Catalyzed Peptide Coupling, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Toyota, K. K. S. Ng, S. Kuninaga, H. Sekizaki, K. Itoh, K. Tanizawa, M. N. G. James
Crystal Structure And Nucleotide Sequence Of An Anionic Trypsin From Chum Salmon (Oncorhynchus Keta) In Comparison With Atlantic Salmon (Salmo Salar) And Bovine Trypsin
J. Mol. Biol. V. 324 391 2002
PubMed-ID: 12445776  |  Reference-DOI: 10.1016/S0022-2836(02)01097-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRYPSIN
    Chains: A
    EC Number: 3.4.21.4
    Organ: PYLORIC CAECA
    Organism Common: CHUM SALMON
    Organism Scientific: ONCORHYNCHUS KETA
    Organism Taxid: 8018

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1BEN1Ligand/IonBENZAMIDINE
2CA1Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:70 , ASN A:72 , VAL A:75 , GLU A:77 , GLU A:80 , HOH A:1248BINDING SITE FOR RESIDUE CA A 1
2AC2SOFTWAREASP A:189 , SER A:190 , CYS A:191 , SER A:195 , GLY A:216 , GLY A:219 , GLY A:226 , HOH A:1237BINDING SITE FOR RESIDUE BEN A 1222

(-) SS Bonds  (6, 6)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1MBQ)

(-) 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:220
 aligned with Q8AV11_ONCKE | Q8AV11 from UniProtKB/TrEMBL  Length:222

    Alignment length:220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
        Q8AV11_ONCKE      1 IVGGYECKAYSQPHQVSLNSGYHFCGGSLVNENWVVSAAHCYKSRVEVRLGEHNIKVTEGSEQFISSSRVIRHPNYSSYNIDNDIMLIKLSKPATLNTYVQPVALPSSCAPAGTMCTVSGWGNTMSSTADKNKLQCLNIPILSYSDCNNSYPGMITNAMFCAGYLEGGKDSCQGDSGGPVVCNGELQGVVSWGYGCAEPGNPGVYAKVCIFNDWLTSTMA  220
               SCOP domains d1mbqa_ A: Trypsin(ogen)                                                                                                                                                                                                     SCOP domains
               CATH domains 1mbqA01     1mbqA02 A:28-120,A:233-243 Trypsin-like serine proteases                                  1mbqA01 A:16-27,A:121-232 Trypsin-like serine proteases                                                    1mbqA02     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeee...eeeeeee....eeeehhhhh....eeee............eeeeeeeeee.............eeeee........................eeeeee..............eeeeee..hhhhhhhhh.......eeee................eeee..eeeeeeee..........eeeee...hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1mbq A   16 IVGGYECKAYSQPHQVSLNSGYHFCGGSLVNENWVVSAAHCYKSRVEVRLGEHNIKVTEGSEQFISSSRVIRHPNYSSYNIDNDIMLIKLSKSATLNTYVQPVALPSSCAPAGTMCTVSGWGNTMSSTADKNKLQCLNIPILSYSDCNNSYPGMITNAMFCAGYLEGGKDSCQGDSGGPVVCNGELQGVVSWGYGCAEPGNPGVYAKVCIFNDWLTSTMA  243
                                    25        37        47        57        67|       78        88        98       108       118      |129||     140       150|      161       171       181  |||  189       199    || 213   || |223       233       243
                                             34|                            67|                                                     125|  ||               150|                             184||  |||            204|     217| |||                     
                                              37                             69                                                      127  ||                152                             1184|  |||             209      219 |||                     
                                                                                                                                        130|                                                  185  |||                        221||                     
                                                                                                                                         132                                                     188||                        1221|                     
                                                                                                                                                                                                 1188|                          222                     
                                                                                                                                                                                                   189
   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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8AV11_ONCKE | Q8AV11)
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:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

 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
    BEN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1mbq)
 

(-) 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
  1mbq
    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
  Q8AV11_ONCKE | Q8AV11
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  Q8AV11_ONCKE | Q8AV11
    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
        Q8AV11_ONCKE | Q8AV11: 2zpr 2zps
UniProtKB/TrEMBL
        Q8AV11_ONCKE | Q8AV11: 2zpq

(-) Related Entries Specified in the PDB File

2tbs ANIONIC TRYPSIN FROM ATLANTIC SALMON