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

(-) Description

Title :  STRUCTURE OF THE COAT PROTEIN IN FD FILAMENTOUS BACTERIOPHAGE PARTICLES
 
Authors :  A. C. Zeri, M. F. Mesleh, A. A. Nevzorov, S. J. Opella
Date :  18 Dec 02  (Deposition) - 06 May 03  (Release) - 24 Feb 09  (Revision)
Method :  SOLID-STATE NMR
Resolution :  NOT APPLICABLE
Chains :  Asym. Unit :  A  (20x)
Keywords :  Alpha Helix, Helical Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. C. Zeri, M. F. Mesleh, A. A. Nevzorov, S. J. Opella
Structure Of The Coat Protein In Fd Filamentous Bacteriophage Particles Determined By Solid-State Nmr Spectroscopy
Proc. Natl. Acad. Sci. Usa V. 100 6458 2003
PubMed-ID: 12750469  |  Reference-DOI: 10.1073/PNAS.1132059100
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MAJOR COAT PROTEIN
    ChainsA
    MutationYES
    Organism ScientificENTEROBACTERIA PHAGE FD
    Organism Taxid10864
    StrainFD

 Structural Features

(-) Chains, Units

  
Asymmetric Unit (20x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1NH4)

(-) Sites  (0, 0)

(no "Site" information available for 1NH4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1NH4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1NH4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NH4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1NH4)

(-) Exons   (0, 0)

(no "Exon" information available for 1NH4)

(-) 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:44
 aligned with Q9T0Q9_BPFD | Q9T0Q9 from UniProtKB/TrEMBL  Length:50

    Alignment length:44
                                    15        25        35        45    
           Q9T0Q9_BPFD    6 PAKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTSKA 49
               SCOP domains d1nh4a_ A:                                   SCOP domains
               CATH domains 1nh4A00 A:6-49                               CATH domains
               Pfam domains Phage_Coat_Gp8-1nh4A01 A:6-49                Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------- PROSITE
                 Transcript -------------------------------------------- Transcript
                  1nh4 A  6 PAKAAFDSLQASATEMIGYAWAMVVVIVGATIGIKLFKKFTSKA 49
                                    15        25        35        45    

   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)

Asymmetric Unit

(-) CATH Domains  (1, 1)

Asymmetric Unit

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q9T0Q9_BPFD | Q9T0Q9)
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.

 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
(no "Ligands, Modified Residues, Ions" information available for 1nh4)
 
  Sites
(no "Sites" information available for 1nh4)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1nh4)
 

(-) 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
  1nh4
    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
  Q9T0Q9_BPFD | Q9T0Q9
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  Q9T0Q9_BPFD | Q9T0Q9
    Protein Disorder PredictionDisEMBL | 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 1NH4)

(-) Related Entries Specified in the PDB File

1ifi FIBER DIFFRACTION STRUCTURE