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(-) Description

Title :  TRYPSIN FROM FUSARIUM OXYSPORUM- ROOM TEMPERATURE TO ATOMIC RESOLUTION
 
Authors :  A. Schmidt, V. S. Lamzin
Date :  28 Oct 04  (Deposition) - 26 Jul 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Atomic Resolution, Mobility, Room Temperature, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Schmidt, V. S. Lamzin
Extraction Of Functional Motion In Trypsin Crystal Structures.
Acta Crystallogr. , Sect. D V. 61 1132 2005
PubMed-ID: 16041079  |  Reference-DOI: 10.1107/S0907444905016732
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRYPSIN
    ChainsA
    EC Number3.4.21.4
    Organism ScientificFUSARIUM OXYSPORUM
    Organism Taxid5507
 
Molecule 2 - SUBSTRATE TRIPEPTIDE GLY-ALA-ARG
    ChainsB
    EngineeredYES
    Other DetailsTHE PEPTIDE IS CHEMICALLY SYNTHESIZED.
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1XVM)

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:41 -A:57
2A:165 -A:180
3A:191 -A:216

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.TRYP_FUSOX25-248  1A:16-239
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.TRYP_FUSOX61-66  1A:52-57
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.TRYP_FUSOX198-209  1A:189-200

(-) Exons   (0, 0)

(no "Exon" information available for 1XVM)

(-) 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:224
 aligned with TRYP_FUSOX | P35049 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:224
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244    
          TRYP_FUSOX     25 IVGGTSASAGDFPFIVSISRNGGPWCGGSLLNANTVLTAAHCVSGYAQSGFQIRAGSLSRTSGGITSSLSSVRVHPSYSGNNNDLAILKLSTSIPSGGNIGYARLAASGSDPVAGSSATVAGWGATSEGGSSTPVNLLKVTVPIVSRATCRAQYGTSAITNQMFCAGVSSGGKDSCQGDSGGPIVDSSNTLIGAVSWGNGCARPNYSGVYASVGALRSFIDTYA  248
               SCOP domains d1xvma_ A: Trypsin(ogen)                                                                                                                                                                                                         SCOP domains
               CATH domains 1xvmA01     1xvmA02 A:28-117,A:230-239 Trypsin-like serine proteases                                  1xvmA01 A:16-27,A:118-229 Trypsin-like serine proteases                                                         1xvmA02    CATH domains
               Pfam domains Trypsin-1xvmA01 A:16-235                                                                                                                                                                                                    ---- Pfam domains
         Sec.struct. author ....ee........eeeeee..eeeeeeeeee..eeeehhhhhh..hhh.eeeee.........eee.eeeeee...........eeeee..........................eeeeee...............eeeeeeeehhhhhhhhhh.......eeee................eeee....eeeeeee..........eeeeehhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-239 UniProt: 25-248                                                                                                                                                                                       PROSITE (1)
                PROSITE (2) ------------------------------------TRYPSI-----------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER --------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1xvm A   16 IVGGTSASAGDFPFIVSISRNGGPWCGGSLLNANTVLTAAHCVSGYAQSGFQIRAGSLSRTSGGITSSLSSVRVHPSYSGNNNDLAILKLSTSIPSGGNIGYARLAASGSDPVAGSSATVAGWGATSEGGSSTPVNLLKVTVPIVSRATCRAQYGTSAITNQMFCAGVSSGGKDSCQGDSGGPIVDSSNTLIGAVSWGNGCARPNYSGVYASVGALRSFIDTYA  239
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235    

Chain B from PDB  Type:PROTEIN  Length:3
                                    
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                1xvm B 2001 GAR 2003

   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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TRYP_FUSOX | P35049)
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: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.
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TRYP_FUSOX | P350491fn8 1fy4 1fy5 1gdn 1gdq 1gdu 1ppz 1pq5 1pq7 1pq8 1pqa 1try 1xvo 2g51 2g52 2vu8

(-) Related Entries Specified in the PDB File

1ppz
1pq5
1pq8
1pqa
1xvo TRYPSIN FROM FUSARIUM OXYSPORUM AT PH 6