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(-) Description

Title :  BENZAMIDINE IN COMPLEX WITH RAT TRYPSIN MUTANT X99/175/190RT
 
Authors :  M. T. Stubbs
Date :  30 Nov 02  (Deposition) - 23 Dec 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Serine Protease, Hydrolase, Serine Proteinase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Reyda, C. Sohn, G. Klebe, K. Rall, D. Ullmann, H. D. Jakubke, M. T. Stubbs
Reconstructing The Binding Site Of Factor Xa In Trypsin Reveals Ligand-Induced Structural Plasticity
J. Mol. Biol. V. 325 963 2003
PubMed-ID: 12527302  |  Reference-DOI: 10.1016/S0022-2836(02)01337-2
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRYPSIN II, ANIONIC
    ChainsA
    EC Number3.4.21.4
    EngineeredYES
    Expression SystemSACCHAROMYCES CEREVISIAE
    Expression System CommonBAKER'S YEAST
    Expression System PlasmidPYT
    Expression System Taxid4932
    Expression System Vector TypePLASMID
    MutationYES
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymTRYPSINOGEN, BETA-TRYPSIN, PRETRYPSINOGEN II
    TissuePANCREAS

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1BEN3Ligand/IonBENZAMIDINE
2CA1Ligand/IonCALCIUM ION
3SO41Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:70 , ASN A:72 , VAL A:75 , GLU A:77 , GLU A:80 , HOH A:261BINDING SITE FOR RESIDUE CA A 480
2AC2SOFTWAREBEN A:1 , HIS A:57 , GLN A:192 , GLY A:193 , SER A:195 , HOH A:726 , HOH A:727BINDING SITE FOR RESIDUE SO4 A 600
3AC3SOFTWAREASP A:189 , ALA A:190 , CYS A:191 , GLN A:192 , SER A:195 , GLY A:216 , GLY A:219 , GLY A:226 , HOH A:502 , SO4 A:600BINDING SITE FOR RESIDUE BEN A 1
4AC4SOFTWAREBEN A:3 , ALA A:221 , PRO A:222BINDING SITE FOR RESIDUE BEN A 2
5AC5SOFTWAREBEN A:2 , TYR A:217 , LEU A:221A , PRO A:222 , ASN A:224BINDING SITE FOR RESIDUE BEN A 3

(-) 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 1J15)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J15)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.TRY2_RAT24-244  1A:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.TRY2_RAT59-64  1A:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.TRY2_RAT194-205  1A:189-200

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000188521ENSRNOE00000331572chr4:69088288-6908832740TRY2_RAT1-14140--
1.2bENSRNOT000000188522bENSRNOE00000277233chr4:69090744-69090903160TRY2_RAT14-67541A:16-61 (gaps)46
1.3ENSRNOT000000188523ENSRNOE00000105498chr4:69092114-69092367254TRY2_RAT67-152861A:61-149 (gaps)89
1.4ENSRNOT000000188524ENSRNOE00000338303chr4:69092772-69092908137TRY2_RAT152-197461A:149-19246
1.5ENSRNOT000000188525ENSRNOE00000134316chr4:69093163-69093367205TRY2_RAT198-246491A:193-245 (gaps)54

(-) 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 TRY2_RAT | P00763 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:223
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243   
            TRY2_RAT     24 IVGGYTCQENSVPYQVSLNSGYHFCGGSLINDQWVVSAAHCYKSRIQVRLGEHNINVLEGNEQFVNAAKIIKHPNFDRKTLNNDIMLIKLSSPVKLNARVATVALPSSCAPAGTQCLISGWGNTLSSGVNEPDLLQCLDAPLLPQADCEASYPGKITDNMVCVGFLEGGKDSCQGDSGGPVVCNGELQGIVSWGYGCALPDNPGVYTKVCNYVDWIQDTIAAN  246
               SCOP domains d1j15a_ A: Trypsin(ogen)                                                                                                                                                                                                        SCOP domains
               CATH domains 1j15A01     1j15A02 A:28-120,A:233-245 Trypsin-like serine proteases                                  1j15A01 A:16-27,A:121-232 Trypsin-like serine proteases                                                     1j15A02       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeee...eeeeeeeee..eeeehhhhh....eeee............eeeeeeeeee.............eeeee........................eeeeee...............eeeeee..hhhhhhh.........eeee................eeee..eeeeeeee..........eeeee...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 24-244                                                                                                                                                                                   -- PROSITE (1)
                PROSITE (2) -----------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ----------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2b  PDB: A:16-61 (gaps) [INCOMPLETE] ------------------------------------------------------------------------------------Exon 1.4  PDB: A:149-192 UniProt: 152-197     Exon 1.5  PDB: A:193-245 (gaps) UniProt: 198-246  Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.3  PDB: A:61-149 (gaps) UniProt: 67-152                                        ---------------------------------------------------------------------------------------------- Transcript 1 (2)
                1j15 A   16 IVGGYTCQENSVPYQVSLNSGYHFCGGSLINDQWVVSAAHCYKSRIQVRLGEHNINVLEGNEQFVNAAKIIKHPNFDRETYNNDIMLIKLSSPVKLNARVATVALPSSCAPAGTQCLISGWGNTLSSGVNEPDLLQCLDAPLLPQADCEASSSFIITDNMVCVGFLEGGKDACQGDSGGPVVCNGELQGIVSWGYGCALPDNPGVYTKVCNYVDWIQDTIAAN  245
                                    25        37        47        57      ||68        78        88        98       108       118      |129||     140       150       160       170       180    | 188A       198     ||212    || 222       232       242   
                                             34|                         64|                                                        125|  ||                                                 184A 188A             204|     217|  |                        
                                              37                          66                                                         127  ||                                                                        209      219  |                        
                                                                                                                                        130|                                                                                   221A                        
                                                                                                                                         132                                                                                                               

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  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  (0, 0)

(no "Pfam Domain" information available for 1J15)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TRY2_RAT | P00763)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0030574    collagen catabolic process    The proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix, usually carried out by proteases secreted by nearby cells.
    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.
    GO:0007584    response to nutrient    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nutrient stimulus.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TRY2_RAT | P007631amh 1anb 1anc 1and 1ane 1bra 1brb 1brc 1co7 1dpo 1ezs 1ezu 1f5r 1f7z 1fy8 1j14 1j16 1j17 1k9o 1ql9 1slu 1slv 1slw 1slx 1trm 1ykt 1ylc 1yld 2trm 3fp6 3fp7 3fp8 3tgi 3tgj 3tgk

(-) Related Entries Specified in the PDB File

1j14 BENZAMIDINE IN COMPLEX WITH RAT TRYPSIN MUTANT X99RT
1j16 BENZAMIDINE IN COMPLEX WITH RAT TRYPSIN MUTANT X99/175/ 190RT AT 100K
1j17 FACTOR XA SPECIFIC INHIBITOR IN COMPLEX WITH RAT TRYPSIN MUTANT X99/175/190RT
1ql7
1ql8
1ql9