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 THE LONG SARAFOTOXIN SRTX-M
 
Authors :  F. Cordier, A. Zorba, M. Hajj, F. Ducancel, D. Servent, M. Delepierre
Date :  24 May 11  (Deposition) - 21 Sep 11  (Release) - 01 Feb 12  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
NMR Structure *:  A  (1x)
Keywords :  Endothelin-Like Peptide, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Mourier, M. Hajj, F. Cordier, A. Zorba, X. Gao, T. Coskun, A. Herbet, E. Marcon, F. Beau, M. Delepierre, F. Ducancel, D. Servent
Pharmacological And Structural Characterization Of Long-Sarafotoxins, A New Family Of Endothelin-Like Peptides Role Of The C-Terminus Extension.
Biochimie V. 94 461 2012
PubMed-ID: 21889567  |  Reference-DOI: 10.1016/J.BIOCHI.2011.08.014

(-) Compounds

Molecule 1 - SARAFOTOXIN-M
    Chains: A
    Engineered: YES
    Organism Common: SNAKES
    Organism Scientific: ATRACTASPIS MICROLEPIDOTA
    Organism Taxid: 172021
    Synonym: SRTX-M
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1
NMR Structure (10x): A
NMR Structure * (1x): A

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2LDF)

(-) SS Bonds  (2, 2)

NMR Structure
No.Residues
1A:1 -A:15
2A:3 -A:11

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ENDOTHELINPS00270 Endothelin family signature.SRTXL_ATRMM30-44
78-92
126-140
174-188
222-236
270-284
318-332		  1-
-
-
-
-
A:1-15
-
NMR Structure * (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ENDOTHELINPS00270 Endothelin family signature.SRTXL_ATRMM30-44
78-92
126-140
174-188
222-236
270-284
318-332		  1-
-
-
-
-
A:1-15
-

(-) Exons   (0, 0)

(no "Exon" information available for 2LDF)

(-) 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:24
 aligned with SRTXL_ATRMM | Q6RY98 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:24
                                   279       289    
          SRTXL_ATRMM   270 CSCNDINDKECMYFCHQDVIWDEP 293
               SCOP domains ------------------------ SCOP domains
               CATH domains ------------------------ CATH domains
               Pfam domains ------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------ SAPs(SNPs)
                    PROSITE ENDOTHELIN     --------- PROSITE
                 Transcript ------------------------ Transcript
                 2ldf A   1 CSCNDINDKECMYFCHQDVIWDEP  24
                                    10        20
   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 2LDF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

NMR Structure(hide GO term definitions)
Chain A   (SRTXL_ATRMM | Q6RY98)
biological process
    GO:0050880    regulation of blood vessel size    Any process that modulates the size of blood vessels.
    GO:0019229    regulation of vasoconstriction    Any process that modulates the frequency, rate or extent of reductions in the diameter of blood vessels.
    GO:0042310    vasoconstriction    A decrease in the diameter of blood vessels, especially arteries, due to constriction of smooth muscle cells that line the vessels, and usually causing an increase in blood pressure.
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

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 2ldf)
 
  Sites
(no "Sites" information available for 2ldf)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ldf)
 

(-) 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
  2ldf
    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
  SRTXL_ATRMM | Q6RY98
    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
  SRTXL_ATRMM | Q6RY98
    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 2LDF)

(-) Related Entries Specified in the PDB File

2lde