Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  FUSARIUM OXYSPORUM TRYPSIN AT ATOMIC RESOLUTION
 
Authors :  W. R. Rypniewski, P. Oestergaard, M. Noerregaard-Madsen, M. Dauter, K
Date :  21 Aug 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
    Chains: A
    EC Number: 3.4.21.4
    Organism Scientific: FUSARIUM OXYSPORUM
    Organism Taxid: 5507
 
Molecule 2 - GLY-ALA-ARG
    Chains: B
    Engineered: YES
    Synthetic: YES

 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:1037 , HOH A:1215 , HOH A:1241 , HOH A:1250 , HOH A:1339 , HOH A:1370BINDING SITE FOR RESIDUE SO4 A 247
2AC2SOFTWAREPRO A:130 , VAL A:131 , ALA A:132 , SER A:164 , ARG A:165 , HOH A:1036 , HOH A:1053 , HOH A:1088 , HOH A:1320BINDING 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:1013 , HOH A:1046 , HOH A:1048 , HOH A:1346BINDING SITE FOR RESIDUE GOL A 244
4AC4SOFTWAREALA A:24 , GLY A:25 , ASP A:26 , PHE A:27 , GLY A:69 , SER A:70 , ASN A:117 , HOH A:1008 , HOH A:1024 , HOH A:1078BINDING 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:1012 , HOH A:1032 , HOH A:1332 , HOH A:1373 , HOH A:1377BINDING 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 , GLY A:219 , GLY A:226 , HOH A:2004 , HOH A:2104 , HOH A:2105 , HOH B:1210 , HOH B:2003 , 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-ARG

(-) 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 1FN8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1FN8)

(-) 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 1FN8)

(-) 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 d1fn8a_ A: Trypsin(ogen)                                                                                                                                                                                                         SCOP domains
               CATH domains 1fn8A01     1fn8A02 A:28-120,A:233-242 Trypsin-like serine proteases                                  1fn8A01 A:16-27,A:121-232 Trypsin-like serine proteases                                                         1fn8A02    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
                1fn8 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
                1fn8 B    1 GAR    3
   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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1FN8)

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1fn8)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1fn8
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  TRYP_FUSOX | P35049
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.21.4
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  TRYP_FUSOX | P35049
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TRYP_FUSOX | P35049: 1fy4 1fy5 1gdn 1gdq 1gdu 1ppz 1pq5 1pq7 1pq8 1pqa 1try 1xvm 1xvo 2g51 2g52 2vu8

(-) Related Entries Specified in the PDB File

1gdn
1try MONOCLINIC CRYSTAL FORM, 1.55A RESOLUTION