Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF C8A/C37A-T1 FROM NICOTIANA ALATA
 
Authors :  H. Schirra, R. F. Guarino, M. A. Anderson, D. J. Craik
Date :  20 Dec 07  (Deposition) - 30 Dec 08  (Release) - 30 Dec 08  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Protein, Proteinase Inhibitor, Pot Ii Inhibitor, Free Form, Hydrolase Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Schirra, R. F. Guarino, M. A. Anderson, D. J. Craik
Selective Removal Of Individual Disulfide Bonds In The Nicotiana Alata Proteinase Inhibitor T1 Reveals Different Stabilisation Of The Reactive Site Loop
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEINASE INHIBITOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: M15
    Expression System Taxid: 562
    Expression System Vector: PCR 2.1 TOPO
    Expression System Vector Type: VECTOR
    Fragment: UNP RESIDUES 112-164
    Mutation: YES
    Organism Common: WINGED TOBACCO
    Organism Scientific: NICOTIANA ALATA
    Organism Taxid: 4087

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2JYY)

(-) Sites  (0, 0)

(no "Site" information available for 2JYY)

(-) SS Bonds  (3, 3)

NMR Structure
No.Residues
1A:4 -A:41
2A:7 -A:25
3A:14 -A:50

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2JYY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2JYY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2JYY)

(-) Exons   (0, 0)

(no "Exon" information available for 2JYY)

(-) Sequences/Alignments

NMR Structure
   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:53
 aligned with Q40378_NICAL | Q40378 from UniProtKB/TrEMBL  Length:397

    Alignment length:53
                                   121       131       141       151       161   
         Q40378_NICAL   112 DRICTNCCAGTKGCKYFSDDGTFVCEGESDPRNPKACPRNCDPRIAYGICPLA 164
               SCOP domains d2jyya_ A: automated matches                          SCOP domains
               CATH domains 2jyyA00 A:1-53  [code=3.30.60.30, no name defined]    CATH domains
           Pfam domains (1) ---------------------------------Prot_inhib_II-2jyyA0 Pfam domains (1)
           Pfam domains (2) ---------------------------------Prot_inhib_II-2jyyA0 Pfam domains (2)
         Sec.struct. author ..............eee.....eeee....................eee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                 2jyy A   1 DRICTNCAAGTKGCKYFSDDGTFVCEGESDPRNPKAAPRNCDPRIAYGICPLA  53
                                    10        20        30        40        50
   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)

NMR Structure
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

NMR Structure
(-)
Clan: no clan defined [family: Prot_inhib_II] (6)

(-) Gene Ontology  (2, 2)

NMR Structure(hide GO term definitions)
Chain A   (Q40378_NICAL | Q40378)
molecular function
    GO:0004867    serine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
    GO:0010951    negative regulation of endopeptidase activity    Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.

 Visualization

(-) Interactive Views

NMR Structure
  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
(no "Ligands, Modified Residues, Ions" information available for 2jyy)
 
  Sites
(no "Sites" information available for 2jyy)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2jyy)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - all models 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
  2jyy
    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
  Q40378_NICAL | Q40378
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  Q40378_NICAL | Q40378
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q40378_NICAL | Q40378: 1ce3 1fyb 1qh2 1tih 1vtp 1ytp 2jzm

(-) Related Entries Specified in the PDB File

1tih WILD-TYPE
1ytp C4A/C41A VARIANT