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(-) Description

Title :  CRYSTAL STRUCTURE OF ANIONIC TRYPSIN ISOFORM 3 FROM CHUM SALMON
 
Authors :  D. Iyaguchi, E. Toyota
Date :  28 Jul 08  (Deposition) - 28 Jul 09  (Release) - 28 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A
Keywords :  Serine Proteinase, Trypsin, Hydrolase, Protease, Serine Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Toyota, D. Iyaguchi, H. Sekizaki, M. Tateyama, K. K. Ng
A Structural Comparison Of Three Isoforms Of Anionic Trypsi From Chum Salmon (Oncorhynchus Keta).
Acta Crystallogr. , Sect. D V. 65 717 2009
PubMed-ID: 19564692  |  Reference-DOI: 10.1107/S0907444909012165

(-) Compounds

Molecule 1 - ANIONIC TRYPSIN
    ChainsA
    Organism CommonCHUM SALMON
    Organism ScientificONCORHYNCHUS KETA
    Organism Taxid8018

 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:52 , ASN A:54 , GLU A:59 , GLU A:62 , HOH A:2018BINDING SITE FOR RESIDUE CA A 2001
2AC2SOFTWAREASP A:170 , SER A:171 , CYS A:172 , SER A:176 , GLY A:193 , GLY A:195 , GLY A:203 , HOH A:2016BINDING SITE FOR RESIDUE BEN A 1001

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:7 -A:136
2A:25 -A:41
3A:109 -A:209
4A:116 -A:182
5A:147 -A:161
6A:172 -A:196

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ZPS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZPS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZPS)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZPS)

(-) 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:221
 aligned with B3Y8K6_ONCKE | B3Y8K6 from UniProtKB/TrEMBL  Length:222

    Alignment length:221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 
         B3Y8K6_ONCKE     1 IVGGYECKAYSQPHQVSLNSGYHFCGGSLVNENWVVSAAHCYKTRVEVRLGEHNIKVTEGSEQFISSSRVIRHPNYSSYNIDNDIMLIKLSKPATLNTYVQPVALPSSCAPAGTMCTVSGWGNTMSSTADKNKLQCLNIPILSYSDCNNSYPGMITNAMFCAGYLEGGKDSCQGDSGGPVVCNGELQGVVSWGYGCAEPGNPGVYAKVCIFNNWLTSTMAT 221
               SCOP domains d2zpsa_ A: automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains 2zpsA01     2zpsA02 A:13-102,A:210-221 Trypsin-like serine proteases                                  2zpsA01 A:1-12,A:103-209 Trypsin-like serine proteases                                                     2zpsA02      CATH domains
               Pfam domains Trypsin-2zpsA01 A:1-215                                                                                                                                                                                                ------ Pfam domains
         Sec.struct. author ....ee........eeeee...eeeeeeeee..eeeehhhhh....eeee............eeeeeeeeee.............eeeee........................eeeeee..............eeeeee..hhhhhhhhh.......eeee................eeee..eeeeeeee..........eeeee...hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zps A   1 IVGGYECKAYSQPHQVSLNSGYHFCGGSLVNENWVVSAAHCYKTRVEVRLGEHNIKVTEGSEQFISSSRVIRHPNYSSYNIDNDIMLIKLSKPATLNTYVQPVALPSSCAPAGTMCTVSGWGNTMSSTADKNKLQCLNIPILSYSDCNNSYPGMITNAMFCAGYLEGGKDSCQGDSGGPVVCNGELQGVVSWGYGCAEPGNPGVYAKVCIFNNWLTSTMAT 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 

Chain A from PDB  Type:PROTEIN  Length:221
 aligned with Q8AV11_ONCKE | Q8AV11 from UniProtKB/TrEMBL  Length:222

    Alignment length:221
                                    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 IVGGYECKAYSQPHQVSLNSGYHFCGGSLVNENWVVSAAHCYKSRVEVRLGEHNIKVTEGSEQFISSSRVIRHPNYSSYNIDNDIMLIKLSKPATLNTYVQPVALPSSCAPAGTMCTVSGWGNTMSSTADKNKLQCLNIPILSYSDCNNSYPGMITNAMFCAGYLEGGKDSCQGDSGGPVVCNGELQGVVSWGYGCAEPGNPGVYAKVCIFNDWLTSTMAT 221
               SCOP domains d2zpsa_ A: automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains 2zpsA01     2zpsA02 A:13-102,A:210-221 Trypsin-like serine proteases                                  2zpsA01 A:1-12,A:103-209 Trypsin-like serine proteases                                                     2zpsA02      CATH domains
               Pfam domains Trypsin-2zpsA01 A:1-215                                                                                                                                                                                                ------ Pfam domains
         Sec.struct. author ....ee........eeeee...eeeeeeeee..eeeehhhhh....eeee............eeeeeeeeee.............eeeee........................eeeeee..............eeeeee..hhhhhhhhh.......eeee................eeee..eeeeeeee..........eeeee...hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zps A   1 IVGGYECKAYSQPHQVSLNSGYHFCGGSLVNENWVVSAAHCYKTRVEVRLGEHNIKVTEGSEQFISSSRVIRHPNYSSYNIDNDIMLIKLSKPATLNTYVQPVALPSSCAPAGTMCTVSGWGNTMSSTADKNKLQCLNIPILSYSDCNNSYPGMITNAMFCAGYLEGGKDSCQGDSGGPVVCNGELQGVVSWGYGCAEPGNPGVYAKVCIFNNWLTSTMAT 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 

   Legend:   → Mismatch (orange background)
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  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  (1, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (6, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (B3Y8K6_ONCKE | B3Y8K6)
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.

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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q8AV11_ONCKE | Q8AV112zpr
UniProtKB/TrEMBL
        Q8AV11_ONCKE | Q8AV111mbq 2zpq

(-) Related Entries Specified in the PDB File

2zpq ISOFORM 1
2zpr ISOFORM 2