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

(-) Description

Title :  THEORETICAL MODEL OF CYTOLYTIC PROTEIN-1 OF BACILLUS THURINGIENSIS LDC-9
 
Authors :  A. Mahalakshmi, K. Sujatha, R. Shenbagarathai
Date :  16 Aug 06  (Deposition) - 17 Aug 06  (Release) - 17 Aug 06  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A
Keywords :  Homology Modeling, Cytolytic Protein, Hemolytic, B. Thuringiensis Ldc-9 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Mahalakshmi, K. Sujatha, R. Shenbagarathai
Theoretical Model Of Cytolytic Protein-1 Of Bacillus Thuringiensis Ldc-9
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOLYTIC INSECTICIDAL PROTEIN 1
    Chains: A
    Engineered: YES
    Fragment: CYTOLYTIC DOMAIN, RESIDUES 9-131
    Other Details: MADURAI COLLECTION OF MICROORGANSIMS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
Theoretical Model : 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2J2D)

(-) Sites  (0, 0)

(no "Site" information available for 2J2D)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2J2D)

(-) Cis Peptide Bonds  (1, 1)

Theoretical Model
No.Residues
1Ile A:53 -Thr A:54

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2J2D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2J2D)

(-) Exons   (0, 0)

(no "Exon" information available for 2J2D)

(-) Sequences/Alignments

Theoretical Model
   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:123
 aligned with Q38PK3_BACTU | Q38PK3 from UniProtKB/TrEMBL  Length:131

    Alignment length:123
                                    18        28        38        48        58        68        78        88        98       108       118       128   
         Q38PK3_BACTU     9 IISNYILQAIMLANAFQNALVPTSTDFGDALRFSMPKGLEIANTITPMGAVVSYVDQNVTQTNNQVSVMINKVLEVLKTVLGVALSGSVIDQLTAAVTNTFTNLNTQKNEAWICWGKETANQT 131
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..............hhhhhhhhhh.....................hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhh............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j2d A   9 IISNYILQAIMLANAFQNALVPTSTDFGDALRFSMPKGLEIANTITPMGAVVSYVDQNVTQTNNQVSVMINKVLEVLKTVLGVALSGSVIDQLTAAVTNTFTNLNTQKNEAWICWGKETANQT 131
                                    18        28        38        48        58        68        78        88        98       108       118       128
   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  (0, 0)

(no "SCOP Domain" information available for 2J2D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2J2D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J2D)

(-) Gene Ontology  (2, 2)

Theoretical Model(hide GO term definitions)
Chain A   (Q38PK3_BACTU | Q38PK3)
biological process
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
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

Theoretical Model
  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 2j2d)
 
  Sites
(no "Sites" information available for 2j2d)
 
  Cis Peptide Bonds
    Ile A:53 - Thr A:54   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Theoretical Model 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
  2j2d
    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
  Q38PK3_BACTU | Q38PK3
    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
  Q38PK3_BACTU | Q38PK3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2J2D)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2J2D)