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 IN THE PRESENCE OF LIPOPOLYSACCHARIDE
 
Authors :  T. Kushibiki, M. Kamiya, T. Aizawa, Y. Kumaki, T. Kikukawa, M. Mizuguch M. Demura, S. I. Kawabata, K. Kawano
Date :  09 Sep 13  (Deposition) - 19 Feb 14  (Release) - 12 Mar 14  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Peptide/Lps, Antimicrobial Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Kushibiki, M. Kamiya, T. Aizawa, Y. Kumaki, T. Kikukawa, M. Mizuguchi, M. Demura, S. I. Kawabata, K. Kawano
Interaction Between Tachyplesin I, An Antimicrobial Peptide Derived From Horseshoe Crab, And Lipopolysaccharide.
Biochim. Biophys. Acta V. 1844 527 2014
PubMed-ID: 24389234  |  Reference-DOI: 10.1016/J.BBAPAP.2013.12.017

(-) Compounds

Molecule 1 - TACHYPLESIN-1
    Chains: A
    Engineered: YES
    Organism Common: CHINESE HORSESHOE CRAB,JAPANESE HORSESHOE CRAB
    Organism Scientific: TACHYPLEUS TRIDENTATUS
    Organism Taxid: 6853
    Other Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED.
    Synonym: TACHYPLESIN I
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x): A
NMR Structure * (1x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

NMR Structure (1, 1)
No.NameCountTypeFull Name
1NH21Mod. Amino AcidAMINO GROUP
NMR Structure * (1, 1)
No.NameCountTypeFull Name
1NH21Mod. Amino AcidAMINO GROUP

(-) Sites  (0, 0)

(no "Site" information available for 2MDB)

(-) 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 2MDB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2MDB)

(-) 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:18
 aligned with TAC1_TACTR | P14213 from UniProtKB/Swiss-Prot  Length:77

    Alignment length:18
                                    33        
            TAC1_TACTR   24 KWCFRVCYRGICYRRCRG 41
               SCOP domains ------------------ SCOP domains
               CATH domains ------------------ CATH domains
               Pfam domains ------------------ Pfam domains
         Sec.struct. author ..eeeee....eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------ SAPs(SNPs)
                    PROSITE ------------------ PROSITE
                 Transcript ------------------ Transcript
                  2mdb A  1 KWCFRVCYRGICYRRCRx 18
                                    10       |
                                            18-NH2
   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 2MDB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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
    NH2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 2mdb)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2mdb)
 

(-) 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
  2mdb
    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 1ma5 1ma6 1wo0 1wo1 2rtv

(-) Related Entries Specified in the PDB File

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