Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - manually
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - manually
NMR Structure - manually  (Jmol Viewer)
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR: SOLUTION STRUCTURES OF PEPTIDES BASED ON THE PHE508 REGION, THE MOST COMMON SITE OF DISEASE-CAUSING DELTA-F508 MUTATION
 
Authors :  M. A. Massiah, Y. H. Ko, P. L. Pedersen, A. S. Mildvan
Date :  26 Apr 99  (Deposition) - 04 May 99  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (13x)
Keywords :  P25_tfe, Cystic Fibrosis, Peptides, Nmr, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. A. Massiah, Y. H. Ko, P. L. Pedersen, A. S. Mildvan
Cystic Fibrosis Transmembrane Conductance Regulator: Solution Structures Of Peptides Based On The Phe508 Region, The Most Common Site Of Disease-Causing Deltaf508 Mutation.
Biochemistry V. 38 7453 1999
PubMed-ID: 10360942  |  Reference-DOI: 10.1021/BI9903603
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR (CFTR))
    ChainsA
    EngineeredYES
    FragmentF508 MUTATION REGION
    Other DetailsP25 PEPTIDE IN TRIFLUROETHANOL
    Other Details - SourceTHE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE IS BASED ON THE PHE508 REGION OF CF TRANSMEMBRANE REGULATOR NUCLEOTIDE BINDING DOMAIN 1.
    SynonymP25
    SyntheticYES

 Structural Features

(-) Chains, Units

  
NMR Structure (13x)

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1CKW)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1CKW)

(-) 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:25
 aligned with CFTR_SHEEP | Q00555 from UniProtKB/Swiss-Prot  Length:1481

    Alignment length:26
                                   506       516      
           CFTR_SHEEP   497 MPGTIKDNIIFGVSYDEYRYRSVIKA 522
               SCOP domains d1ckwa_ A:                 SCOP domains
               CATH domains -------------------------- CATH domains
               Pfam domains -------------------------- Pfam domains
         Sec.struct. author ...hhhhhhh-hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------- SAPs(SNPs)
                    PROSITE -------------------------- PROSITE
                 Transcript -------------------------- Transcript
                 1ckw A   1 MPGTIKENII-GVSYDEYRYRSVIKA  25
                                    10 |      19      
                                    10 |              
                                      11              

   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 1CKW)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (27, 27)

NMR Structure(hide GO term definitions)
Chain A   (CFTR_SHEEP | Q00555)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0042626    ATPase activity, coupled to transmembrane movement of substances    Catalysis of the reaction: ATP + H2O = ADP + phosphate, to directly drive the active transport of a substance across a membrane.
    GO:0015106    bicarbonate transmembrane transporter activity    Enables the transfer of bicarbonate from one side of a membrane to the other. Bicarbonate is the hydrogencarbonate ion, HCO3-.
    GO:0005254    chloride channel activity    Enables the facilitated diffusion of a chloride (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
    GO:0019869    chloride channel inhibitor activity    Stops, prevents, or reduces the activity of a chloride channel.
    GO:0015108    chloride transmembrane transporter activity    Enables the transfer of chloride ions from one side of a membrane to the other.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0005260    intracellular ATPase-gated chloride channel activity    Enables passage of a chloride ion through a transmembrane channel that opens when intracellular ATP is bound and hydrolysed. Passage is via passive diffusion once the channel is open.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0015701    bicarbonate transport    The directed movement of bicarbonate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0071320    cellular response to cAMP    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate) stimulus.
    GO:1902476    chloride transmembrane transport    The directed movement of chloride across a membrane.
    GO:0006821    chloride transport    The directed movement of chloride into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0051454    intracellular pH elevation    Any process that increases the internal pH of a cell, measured by the concentration of the hydrogen ion.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0060081    membrane hyperpolarization    The process in which membrane potential increases with respect to its steady-state potential, usually from negative potential to a more negative potential. For example, during the repolarization phase of an action potential the membrane potential often becomes more negative or hyperpolarized before returning to the steady-state resting potential.
    GO:0048240    sperm capacitation    A process required for sperm to reach fertilization competence. Sperm undergo an incompletely understood series of morphological and molecular maturational processes, termed capacitation, involving, among other processes, protein tyrosine phosphorylation and increased intracellular calcium.
    GO:0055085    transmembrane transport    The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0034707    chloride channel complex    An ion channel complex through which chloride ions pass.
    GO:0005769    early endosome    A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
    GO:0031901    early endosome membrane    The lipid bilayer surrounding an early endosome.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    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:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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

(-) 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
  1ckw
    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
  CFTR_SHEEP | Q00555
    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
  CFTR_SHEEP | Q00555
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CFTR_SHEEP | Q005551ckx 1cky 1ckz

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1CKW)