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

(-) Description

Title :  STRUCTURES OF PRODUCT AND INHIBITOR COMPLEXES OF STREPTOMYCES GRISEUS PROTEASE A AT 1.8 ANGSTROMS RESOLUTION. A MODEL FOR SERINE PROTEASE CATALYSIS
 
Authors :  A. R. Sielecki, M. N. G. James
Date :  29 May 90  (Deposition) - 15 Oct 91  (Release) - 19 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  E,P
Keywords :  Hydrolase-Hydrolase Inhibitor Complex, Serine Proteinase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. N. James, A. R. Sielecki, G. D. Brayer, L. T. Delbaere, C. A. Bauer
Structures Of Product And Inhibitor Complexes Of Streptomyces Griseus Protease A At 1. 8 A Resolution. A Mode For Serine Protease Catalysis.
J. Mol. Biol. V. 144 43 1980
PubMed-ID: 6783761  |  Reference-DOI: 10.1016/0022-2836(80)90214-4
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEINASE A (SGPA)
    Chains: E
    Engineered: YES
    Gene: SPRA
    Organism Scientific: STREPTOMYCES GRISEUS
    Organism Taxid: 1911
 
Molecule 2 - ACE-PRO-ALA-PRO-PHE-ALDEHYDE
    Chains: P
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : EP

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2PHL1Mod. Amino AcidL-PHENYLALANINOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS E:57 , ASN E:170 , TYR E:171 , ALA E:192 , GLN E:192A , GLY E:193 , SER E:195 , SER E:214 , GLY E:215 , GLY E:216BINDING SITE FOR CHAIN P OF ACE-PRO-ALA-PRO-PHE- ALDEHYDE

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1E:42 -E:58
2E:191 -E:220

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe E:94 -Pro E:99A

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SGA)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.PRTA_STRGR145-150  1E:53-58
2TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.PRTA_STRGR247-258  1E:191-200

(-) Exons   (0, 0)

(no "Exon" information available for 3SGA)

(-) 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 E from PDB  Type:PROTEIN  Length:181
 aligned with PRTA_STRGR | P00776 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:181
                                   126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296 
          PRTA_STRGR    117 IAGGEAITTGGSRCSLGFNVSVNGVAHALTAGHCTNISASWSIGTRTGTSFPNNDYGIIRHSNPAAADGRVYLYNGSYQDITTAGNAFVGQAVQRSGSTTGLRSGSVTGLNATVNYGSSGIVYGMIQTNVCAEPGDSGGSLFAGSTALGLTSGGSGNCRTGGTTFYQPVTEALSAYGATVL  297
               SCOP domains d3sgae_ E: Protease A                                                                                                                                                                 SCOP domains
               CATH domains 3sgaE01 E:16-115,E:231-242 Trypsin-like serine proteases            3sgaE02 E:116-230 Trypsin-like serine proteases                                                     3sgaE01       CATH domains
               Pfam domains --------------------------------------Trypsin-3sgaE01 E:65-236                                                                                                                 ------ Pfam domains
         Sec.struct. author eeeeeeeee.eeeeeeeeeeee..eeeeee.hhhhhh.eee..eeeeeee......eeeee......eeeeee...eeeee.eee.....eeeeeee........eeeeeeeeeee...eeeeeeeee..........eeeee.eeeeeeeeeeeee...eeeeeeehhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------TRYPSI------------------------------------------------------------------------------------------------TRYPSIN_SER --------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3sga E   16 IAGGEAITTGGSRCSLGFNVSVNGVAHALTAGHCTNISASWSIGTRTGTSFPNNDYGIIRHSNPAAADGRVYLYNGSYQDITTAGNAFVGQAVQRSGSTTGLRSGSVTGLNATVNYGSSGIVYGMIQTNVCAQPGDSGGSLFAGSTALGLTSGGSGNCRTGGTTFYQPVTEALSAYGATVL  242
                               ||   34|       48||||    54    || 65A||      93||     107       117   ||||123       133       143|      165       175       190  ||   198   ||  212       222       232   |   241 
                              19|   34|       48A|||         59| 65A||     91|||                  120A|||                    143|                         184|  ||       202|                         235A       
                               29    39        48B||          62   66|      93||                   120B||                     156                          190  ||        207                                    
                                                48C|                84       94|                    120C|                                                    192A|                                               
                                                 48D                         99A                     120D                                                     192B                                               


Chain P from PDB  Type:PROTEIN  Length:5
                                      
               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
                3sga P    5 xPAPf    9
                            |   |
                            5-ACE
                                9-PHL
   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  (1, 1)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain E   (PRTA_STRGR | P00776)
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
    ACE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PHL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Phe E:94 - Pro E:99A  [ RasMol ]  
 

(-) 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
  3sga
    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
  PRTA_STRGR | P00776
    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)
  (no 'Enzyme Classificator' available)
    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
  PRTA_STRGR | P00776
    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
        PRTA_STRGR | P00776: 1sgc 2sga 4sga 5sga

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3SGA)