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(-) Description

Title :  FUSARIUM OXYSPORUM TRYPSIN AT ATOMIC RESOLUTION
 
Authors :  W. R. Rypniewski, P. Oestergaard, M. Noerregaard-Madsen, M. Dauter, K
Date :  28 Sep 00  (Deposition) - 07 Feb 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.81
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta Barrel, Hydrolase, Hydrolase-Hydrolase Substrate Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. R. Rypniewski, P. R. Ostergaard, M. Norregaard-Madsen, M. Dauter, K. S. Wilson
Fusarium Oxysporum Trypsin At Atomic Resolution At 100 And 283 K: A Study Of Ligand Binding.
Acta Crystallogr. , Sect. D V. 57 8 2001
PubMed-ID: 11134922  |  Reference-DOI: 10.1107/S0907444900014116
(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 - GLY-ALA-LYS
    ChainsB
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:40 , ARG A:73 , SER A:93 , HOH A:1028 , HOH A:1227 , HOH A:1250 , HOH A:1298 , HOH A:1303 , HOH A:1321BINDING SITE FOR RESIDUE SO4 A 247
2AC2SOFTWAREASP A:129 , PRO A:130 , VAL A:131 , ALA A:132 , SER A:164 , ARG A:165 , HOH A:1038 , HOH A:1053 , HOH A:1075 , HOH A:1209 , HOH A:1374BINDING SITE FOR RESIDUE GOL A 243
3AC3SOFTWARESER A:21 , GLY A:127 , ASP A:129 , ASN A:154 , ARG A:165 , ASN A:178 , HOH A:1015 , HOH A:1042 , HOH A:1068 , HOH A:1132 , HOH A:1309 , HOH A:1361 , HOH A:1411BINDING SITE FOR RESIDUE GOL A 244
4AC4SOFTWAREALA A:24 , GLY A:25 , ASP A:26 , SER A:70 , ASN A:117 , HOH A:1009 , HOH A:1023 , HOH A:1083BINDING SITE FOR RESIDUE GOL A 245
5AC5SOFTWAREASP A:26 , PHE A:27 , GLY A:59B , TYR A:59C , VAL A:200 , ASN A:203 , HOH A:1032 , HOH A:1357BINDING SITE FOR RESIDUE GOL A 246
6AC6SOFTWAREHIS A:57 , ASP A:189 , SER A:190 , CYS A:191 , GLN A:192 , GLY A:193 , ASP A:194 , SER A:195 , SER A:214 , TRP A:215 , GLY A:216 , HOH A:2104 , HOH B:1289 , HOH B:2003 , HOH B:2004 , HOH B:2005 , HOH B:2006 , HOH B:2101 , HOH B:2102 , HOH B:2103 , HOH B:2201 , HOH B:2202 , HOH B:2204BINDING SITE FOR CHAIN B OF GLY-ALA-LYS

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:42 -A:58
2A:168 -A:182
3A:191 -A:220

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.TRYP_FUSOX25-248  1A:16-242
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.TRYP_FUSOX61-66  1A:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.TRYP_FUSOX198-209  1A:189-200

(-) Exons   (0, 0)

(no "Exon" information available for 1GDN)

(-) 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 d1gdna_ A: Trypsin(ogen)                                                                                                                                                                                                         SCOP domains
               CATH domains 1gdnA01     1gdnA02 A:28-120,A:233-242 Trypsin-like serine proteases                                  1gdnA01 A:16-27,A:121-232 Trypsin-like serine proteases                                                         1gdnA02    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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:16-242 UniProt: 25-248                                                                                                                                                                                       PROSITE (1)
                PROSITE (2) ------------------------------------TRYPSI-----------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER --------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1gdn A   16 IVGGTSASAGDFPFIVSISRNGGPWCGGSLLNANTVLTAAHCVSGYAQSGFQIRAGSLSRTSGGITSSLSSVRVHPSYSGNNNDLAILKLSTSIPSGGNIGYARLAASGSDPVAGSSATVAGWGATSEGGSSTPVNLLKVTVPIVSRATCRAQYGTSAITNQMFCAGVSSGGKDSCQGDSGGPIVDSSNTLIGAVSWGNGCARPNYSGVYASVGALRSFIDTYA  242
                                    25        35|       46        56   |||| 62   |||  73  ||    86        96|      108       118       128       138       148       158       168     | 177       186  |    195      |204|      219  |    228       238    
                                              35|                    59A|||    65A||     76|              96|                                                                       173A        184A 188A          201A  ||     217|  |                     
                                               37                     59B||      66|      80               99                                                                                                          204|      219  |                     
                                                                       59C|       69                                                                                                                                    209        221A                     
                                                                        59D                                                                                                                                                                                 

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
                1gdn B    1 GAK    3

   Legend:   → Mismatch (orange background)
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    → 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  (0, 0)

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

(-) 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 1gdq 1gdu 1ppz 1pq5 1pq7 1pq8 1pqa 1try 1xvm 1xvo 2g51 2g52 2vu8

(-) Related Entries Specified in the PDB File

1fn8 TRICLINIC, ARG-SOAKED, 0.81A RESOLUTION
1try MONOCLINIC CRYSTAL FORM, 1.55A RESOLUTION