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 :  NMR STRUCTURE OF MICROPLUSIN A ANTIMICROBIAL PEPTIDE FROM RHIPICEPHALUS (BOOPHILUS) MICROPLUS
 
Authors :  J. R. Pires, C. A. Rezende, F. D. Silva, S. Daffre
Date :  26 Aug 09  (Deposition) - 13 Oct 09  (Release) - 26 Jan 10  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (15x)
Keywords :  Antimicrobial Peptide, Microplusin, Rhipicephalus (Boophilus) Microplus, Antimicrobial Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. D. Silva, C. A. Rezende, D. C. Rossi, E. Esteves, F. H. Dyszy, S. Schreier, F. Gueiros-Filho, C. B. Campos, J. R. Pires, S. Daffre
Structure And Mode Of Action Of Microplusin, A Copper Ii-Chelating Antimicrobial Peptide From The Cattle Tick Rhipicephalus (Boophilus) Microplus.
J. Biol. Chem. V. 284 34735 2009
PubMed-ID: 19828445  |  Reference-DOI: 10.1074/JBC.M109.016410
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MICROPLUSIN PREPROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Variant: DE3
    Expression System Vector: PRSET-A
    Fragment: UNP RESIDUES 21-110
    Organism Common: CATTLE TICK
    Organism Scientific: RHIPICEPHALUS MICROPLUS
    Organism Taxid: 6941

 Structural Features

(-) Chains, Units

  
NMR Structure (15x): 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2KNJ)

(-) SS Bonds  (3, 3)

NMR Structure
No.Residues
1A:6 -A:52
2A:19 -A:80
3A:41 -A:46

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2KNJ)

(-) 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:90
 aligned with MPSIN_RHIMP | Q86LE5 from UniProtKB/Swiss-Prot  Length:110

    Alignment length:90
                                    30        40        50        60        70        80        90       100       110
          MPSIN_RHIMP    21 HHQELCTKGDDALVTELECIRLRISPETNAAFDNAVQQLNCLNRACAYRKMCATNNLEQAMSVYFTNEQIKEIHDAATACDPEAHHEHDH 110
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhh....hhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 2knj A   1 HHQELCTKGDDALVTELECIRLRISPETNAAFDNAVQQLNCLNRACAYRKMCATNNLEQAMSVYFTNEQIKEIHDAATACDPEAHHEHDH  90
                                    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  (0, 0)

(no "SCOP Domain" information available for 2KNJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

NMR Structure(hide GO term definitions)
Chain A   (MPSIN_RHIMP | Q86LE5)
molecular function
    GO:0016531    copper chaperone activity    Assists in the delivery of copper ions to target proteins or compartments.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046911    metal chelating activity    The formation of bonds from two or more atoms within the same ligand to a metal atom in complexes in which the metal is part of a ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0050830    defense response to Gram-positive bacterium    Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0050832    defense response to fungus    Reactions triggered in response to the presence of a fungus that act to protect the cell or organism.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0031640    killing of cells of other organism    Any process in an organism that results in the killing of cells of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.
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 2knj)
 
  Sites
(no "Sites" information available for 2knj)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2knj)
 

(-) 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
  2knj
    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
  MPSIN_RHIMP | Q86LE5
    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
  MPSIN_RHIMP | Q86LE5
    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 2KNJ)

(-) Related Entries Specified in the PDB File

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