Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  SOLID-STATE NMR STRUCTURE OF PISCIDIN 3 IN ALIGNED 3:1 PHOSPHATIDYLCHOLINE/PHOSPHOGLYCEROL LIPID BILAYERS
 
Authors :  R. Fu, Y. Tian, B. S. Perrin Jr. , C. V. Grant, R. W. Pastor, M. L. Cotten
Date :  27 Aug 13  (Deposition) - 22 Jan 14  (Release) - 19 Mar 14  (Revision)
Method :  SOLID-STATE NMR
Resolution :  NOT APPLICABLE
Chains :  Asym. Unit :  A  (10x)
Biol. Unit 1:  A  (1x)
Keywords :  Antimicrobial Peptide, Cationic, Amphipathic, Histidine Rich, Helical, Lipid Bilayers, Bacterial Cell Membrane Mimic, Antimicrobial Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. S. Perrin, Y. Tian, R. Fu, C. V. Grant, E. Y. Chekmenev, W. E. Wieczorek, A. E. Dao, R. M. Hayden, C. M. Burzynski, R. M. Venable, M. Sharma, S. J. Opella, R. W. Pastor, M. L. Cotten
High-Resolution Structures And Orientations Of Antimicrobia Peptides Piscidin 1 And Piscidin 3 In Fluid Bilayers Reveal Tilting, Kinking, And Bilayer Immersion.
J. Am. Chem. Soc. V. 136 3491 2014
PubMed-ID: 24410116  |  Reference-DOI: 10.1021/JA411119M

(-) Compounds

Molecule 1 - PISCIDIN-3
    Chains: A
    Engineered: YES
    Organism Common: WHITE BASS X STRIPED BASS
    Organism Scientific: MORONE CHRYSOPS X MORONE SAXATILIS
    Organism Taxid: 45352
    Other Details: SYNTHETIC CONSTRUCT
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit (10x): A
Biological Unit 1 (1x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NH21Mod. Amino AcidAMINO GROUP
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NH21Mod. Amino AcidAMINO GROUP

(-) Sites  (0, 0)

(no "Site" information available for 2MCW)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2MCW)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2MCW)

(-) Sequences/Alignments

Asymmetric Unit
   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:23
 aligned with PISC3_MORCS | P0C006 from UniProtKB/Swiss-Prot  Length:22

    Alignment length:23
                                                22     
                                    10        20 | 
           PISC3_MORCS    1 FIHHIFRGIVHAGRSIGRFLTG-  -
               SCOP domains ----------------------- SCOP domains
               CATH domains ----------------------- CATH domains
               Pfam domains ----------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------- SAPs(SNPs)
                    PROSITE ----------------------- PROSITE
                 Transcript ----------------------- Transcript
                  2mcw A  1 FIHHIFRGIVHAGRSIGRFLTGx 23
                                    10        20  |
                                                 23-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 2MCW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (PISC3_MORCS | P0C006)
molecular function
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
biological process
    GO:0019835    cytolysis    The rupture of cell membranes and the loss of cytoplasm.
    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:0044179    hemolysis in other organism    The cytolytic destruction of red blood cells, with the release of intracellular hemoglobin, in one organism by another.
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.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

 Visualization

(-) Interactive Views

Asymmetric Unit
  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 2mcw)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2mcw)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 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
  2mcw
    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
  PISC3_MORCS | P0C006
    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
  PISC3_MORCS | P0C006
    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
        PISC3_MORCS | P0C006: 2mcx

(-) Related Entries Specified in the PDB File

2jos PISCIDIN 1 IN DPC MICELLES
2mcu
2mcv
2mcx RELATED ID: 19456 RELATED DB: BMRB
2ojm PISCIDIN 1 IN SDS MICELLES