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 WILD TYPE PEPTIDE NMR STRUCTURE
 
Authors :  A. Laederach, A. H. Andreotti, D. B. Fulton
Date :  31 Jul 02  (Deposition) - 16 Oct 02  (Release) - 03 Nov 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (31x)
Keywords :  Tachyplesin, Beta Hairpin, Disulfide Bridge, Anti-Microbial Peptide, 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 Aromatic 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 I
    ChainsA
    EngineeredYES
    Other DetailsTHE PEPTIDE WAS CHEMICALLY SYNTHESIZED USING FMOC SOLID STATE SYNTHESIS. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN TACHYPLEUS TRIDENTATUS (JAPANESE HORESHOE CRAB).
    SyntheticYES

 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 1MA2)

(-) Sites  (0, 0)

(no "Site" information available for 1MA2)

(-) 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 1MA2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1MA2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1MA2)

(-) Exons   (0, 0)

(no "Exon" information available for 1MA2)

(-) 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 d1ma2a_ A:        SCOP domains
               CATH domains ----------------- CATH domains
               Pfam domains ----------------- Pfam domains
         Sec.struct. author .....eee..eee.... Sec.struct. author
                 SAPs(SNPs) ----------------- SAPs(SNPs)
                    PROSITE ----------------- PROSITE
                 Transcript ----------------- Transcript
                  1ma2 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 1MA2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1MA2)

(-) 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 1ma2)
 
  Sites
(no "Sites" information available for 1ma2)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ma2)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1ma2
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  TAC1_TACTR | P14213
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  TAC1_TACTR | P14213
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TAC1_TACTR | P142131ma4 1ma5 1ma6 1wo0 1wo1 2mdb 2rtv

(-) Related Entries Specified in the PDB File

1ma4 TPY4 SOLUTION STRUCTURE IN WATER
1ma5 TACHYPLESIN I IN THE PRESENCE OF DODECYLPHOSPHOCHOLINE MICELLES
1ma6 TPY4 TACHYPLESIN I TYROSINE MUTANT IN THE PRESENCE OF DODECYLPHOSPHOCHOLINE MICELLES