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

(-) Description

Title :  BETA-CINNAMOMIN AFTER STEROL REMOVAL
 
Authors :  M. L. Rodrigues, M. Archer, P. Martel, S. Miranda, M. Thomaz, F. J. Enguita, R. P. Baptista, E. P. Melo, N. Sousa, A. Cravador, M. A. Carrondo
Date :  08 Jul 05  (Deposition) - 17 Jan 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Elicitin, Sterol Carrier Protein, Phytophthora, Phytopathogen, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. L. Rodrigues, M. Archer, P. Martel, S. Miranda, M. Thomaz, F. J. Enguita, R. P. Baptista, E. P. Melo, N. Sousa, A. Cravador, M. A. Carrondo
Crystal Structures Of The Free And Sterol-Bound Forms Of Beta-Cinnamomin
Biochim. Biophys. Acta V. 1764 110 2006
PubMed-ID: 16249127  |  Reference-DOI: 10.1016/J.BBAPAP.2005.09.008
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-ELICITIN CINNAMOMIN
    Chains: A, B
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Plasmid: PIC9K
    Expression System Strain: SMD1168
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Gene: CIN1B
    Organism Scientific: PHYTOPHTHORA CINNAMOMI
    Organism Taxid: 4785

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2A8F)

(-) Sites  (0, 0)

(no "Site" information available for 2A8F)

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:3 -A:71
2A:27 -A:56
3A:51 -A:95
4B:3 -B:71
5B:27 -B:56
6B:51 -B:95

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2A8F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2A8F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2A8F)

(-) Exons   (0, 0)

(no "Exon" information available for 2A8F)

(-) 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:98
 aligned with ELIB_PHYCI | P15569 from UniProtKB/Swiss-Prot  Length:98

    Alignment length:98
                                    10        20        30        40        50        60        70        80        90        
            ELIB_PHYCI    1 TACTATQQTAAYKTLVSILSESSFSQCSKDSGYSMLTATALPTNAQYKLMCASTACNTMIKKIVALNPPDCDLTVPTSGLVLDVYTYANGFSSKCASL 98
               SCOP domains d2a8fa_ A: beta-cinnamomin                                                                         SCOP domains
               CATH domains 2a8fA00 A:1-98 Beta-cryptogein                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh.....eee......eeehhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                  2a8f A  1 TACTATQQTAAYKTLVSILSESSFSQCSKDSGYSMLTATALPTNAQYKLMCASTACNTMIKKIVALNPPDCDLTVPTSGLVLDVYTYANGFSSKCASL 98
                                    10        20        30        40        50        60        70        80        90        


Chain B from PDB  Type:PROTEIN  Length:98
 aligned with ELIB_PHYCI | P15569 from UniProtKB/Swiss-Prot  Length:98

    Alignment length:98
                                    10        20        30        40        50        60        70        80        90        
            ELIB_PHYCI    1 TACTATQQTAAYKTLVSILSESSFSQCSKDSGYSMLTATALPTNAQYKLMCASTACNTMIKKIVALNPPDCDLTVPTSGLVLDVYTYANGFSSKCASL 98
               SCOP domains d2a8fb_ B: beta-cinnamomin                                                                         SCOP domains
               CATH domains 2a8fB00 B:1-98 Beta-cryptogein                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh.....eee......eeehhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                  2a8f B  1 TACTATQQTAAYKTLVSILSESSFSQCSKDSGYSMLTATALPTNAQYKLMCASTACNTMIKKIVALNPPDCDLTVPTSGLVLDVYTYANGFSSKCASL 98
                                    10        20        30        40        50        60        70        80        90
   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, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2A8F)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ELIB_PHYCI | P15569)
molecular function
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0005496    steroid binding    Interacting selectively and non-covalently with a steroid, any of a large group of substances that have in common a ring system based on 1,2-cyclopentanoperhydrophenanthrene.
biological process
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:0006869    lipid transport    The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0034053    modulation by symbiont of host defense-related programmed cell death    Any process in which an organism modulates the frequency, rate or extent of defense-related programmed cell death in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    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.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
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
(no "Ligands, Modified Residues, Ions" information available for 2a8f)
 
  Sites
(no "Sites" information available for 2a8f)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2a8f)
 

(-) 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 ](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
  2a8f
    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
  ELIB_PHYCI | P15569
    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
  ELIB_PHYCI | P15569
    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
        ELIB_PHYCI | P15569: 1ljp 2aib

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2A8F)