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(-) Description

Title :  TRYPSIN WITH PMSF AT ATOMIC RESOLUTION
 
Authors :  A. Schmidt, C. Jelsch, W. Rypniewski, V. S. Lamzin
Date :  18 Jun 03  (Deposition) - 11 Nov 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.23
Chains :  Asym./Biol. Unit :  A
Keywords :  Trypsin, Atomic Resolution, Pmsf, Catalysis, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Schmidt, C. Jelsch, P. Ostergaard, W. Rypniewski, V. S. Lamzin
Trypsin Revisited: Crystallography At (Sub) Atomic Resolution And Quantum Chemistry Revealing Details Of Catalysis.
J. Biol. Chem. V. 278 43357 2003
PubMed-ID: 12937176  |  Reference-DOI: 10.1074/JBC.M306944200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRYPSIN
    Chains: A
    EC Number: 3.4.21.4
    Organism Scientific: FUSARIUM OXYSPORUM
    Organism Taxid: 5507

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1SEB1Mod. Amino AcidO-BENZYLSULFONYL-SERINE
2SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:63 , SER A:64 , GLY A:113 , HOH A:456 , HOH A:462 , HOH A:580BINDING SITE FOR RESIDUE SO4 A 401
2AC2SOFTWAREARG A:88 , PRO A:158 , VAL A:183 , SER A:184 , TYR A:238 , HOH A:478 , HOH A:663BINDING SITE FOR RESIDUE SO4 A 402

(-) 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 1PQA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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 1PQA)

(-) 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 d1pqaa_ A: Trypsin(ogen)                                                                                                                                                                                                         SCOP domains
               CATH domains 1pqaA01     1pqaA02 A:28-117,A:230-238 Trypsin-like serine proteases                                  1pqaA01 A:16-27,A:118-229 Trypsin-like serine proteases                                                         1pqaA02  - CATH domains
               Pfam domains Trypsin-1pqaA01 A:16-235                                                                                                                                                                                                    ---- Pfam domains
         Sec.struct. author ....ee........eeeeee..eeeeeeeeee..eeeehhhhhh..hhh.eeeee.........eee.eeeeee...........eeeee..........................eeeeee...............eeeeeeeehhhhhhhhhh.......eeee................eee.....eeeeeee..........eeeee...hhhhhhhhh 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
                 1pqa 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    
                                                                                                                                                                                                             195-SEB
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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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_PA (797)

(-) 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 | P35049: 1fn8 1fy4 1fy5 1gdn 1gdq 1gdu 1ppz 1pq5 1pq7 1pq8 1try 1xvm 1xvo 2g51 2g52 2vu8

(-) Related Entries Specified in the PDB File

1gdn 1gdq 1ppz 1pq5 1pq7 1pq8