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 :  TACHYPLESIN I SOLUTION STRUCTURE IN THE PRESENCE OF 300MM DODECYLPHOSPHOCHOLINE MICELLES
 
Authors :  A. Laederach, A. H. Andreotti, D. B. Fulton
Date :  31 Jul 02  (Deposition) - 16 Oct 02  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (31x)
Keywords :  Tachyplesin I, Beta Hairpin, Dodecylphosphocholine, Conformational Rearrangement, Antimicrobial Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Laederach, A. H. Andreotti, D. B. Fulton
Solution And Micelle-Bound Structures Of Tachyplesin I And Its Active Linear Derivatives
Biochemistry V. 41 12359 2002
PubMed-ID: 12369825  |  Reference-DOI: 10.1021/BI026185Z
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TACHYPLESIN 1
    Chains: A
    Engineered: YES
    Other Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED USING FMOC SOLID STATE SYNTHESIS. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN TACHYPLEUS TRIDENTATUS (JAPANESE HORESHOE CRAB).
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure (31x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1MA5)

(-) Sites  (0, 0)

(no "Site" information available for 1MA5)

(-) SS Bonds  (2, 2)

NMR Structure
No.Residues
1A:3 -A:16
2A:7 -A:12

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1MA5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1MA5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1MA5)

(-) Exons   (0, 0)

(no "Exon" information available for 1MA5)

(-) 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:17
 aligned with TAC1_TACTR | P14213 from UniProtKB/Swiss-Prot  Length:77

    Alignment length:17
                                    33       
            TAC1_TACTR   24 KWCFRVCYRGICYRRCR 40
               SCOP domains d1ma5a_ A:        SCOP domains
               CATH domains ----------------- CATH domains
               Pfam domains ----------------- Pfam domains
         Sec.struct. author ................. Sec.struct. author
                 SAPs(SNPs) ----------------- SAPs(SNPs)
                    PROSITE ----------------- PROSITE
                 Transcript ----------------- Transcript
                  1ma5 A  1 KWCFRVCYRGICYRRCR 17
                                    10
   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: Peptides (792)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1MA5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1MA5)

(-) Gene Ontology  (2, 2)

NMR Structure(hide GO term definitions)
Chain A   (TAC1_TACTR | P14213)
biological process
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or 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

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 1ma5)
 
  Sites
(no "Sites" information available for 1ma5)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ma5)
 

(-) 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
  1ma5
    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
  TAC1_TACTR | P14213
    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
  TAC1_TACTR | P14213
    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
        TAC1_TACTR | P14213: 1ma2 1ma4 1ma6 1wo0 1wo1 2mdb 2rtv

(-) Related Entries Specified in the PDB File

1ma2 TACHYPLESIN I SOLUTION STRUCTURE IN WATER
1ma4 TPY4 TYROSINE MUTANT OF TACHYPLESIN I IN WATER
1ma6 TPY4 TACHYPLESIN I TYROSINE MUTANT IN THE PRESENCE OF DODECYLPHOSPHOCHOLINE MICELLES