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(-) Description

Title :  STRUCTURE OF NBD1 FROM MURINE CFTR- F508R MUTANT
 
Authors :  P. H. Thibodeau, C. A. Brautigam, M. Machius, P. J. Thomas
Date :  14 Sep 04  (Deposition) - 28 Dec 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Cystic Fibrosis, Abc Transporters, Atp, Nucleotide-Binding Domain, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. H. Thibodeau, C. A. Brautigam, M. Machius, P. J. Thomas
Side Chain And Backbone Contributions Of Phe508 To Cftr Folding.
Nat. Struct. Mol. Biol. V. 12 10 2005
PubMed-ID: 15619636  |  Reference-DOI: 10.1038/NSMB881
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPSMT3-NBD1-F508R
    Expression System StrainBL21(DE3) CODON PLUS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentNBD1
    GeneCFTR, ABCC7
    MutationYES
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymCFTR, CAMP-DEPENDENT CHLORIDE CHANNEL

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1ACY4Ligand/IonACETIC ACID
2ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
3CL2Ligand/IonCHLORIDE ION
4MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
3CL-1Ligand/IonCHLORIDE ION
4MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
3CL-1Ligand/IonCHLORIDE ION
4MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREATP A:1 , THR A:465 , GLN A:493BINDING SITE FOR RESIDUE MG A 3
02AC2SOFTWAREATP B:2 , THR B:465 , GLN B:493 , ASP B:572BINDING SITE FOR RESIDUE MG B 4
03AC3SOFTWARELEU A:548 , SER A:549 , GLY A:550 , ARG A:553 , VAL B:546 , THR B:547 , LEU B:548BINDING SITE FOR RESIDUE CL A 5
04AC4SOFTWAREVAL A:546 , THR A:547 , LEU A:548 , LEU B:548 , GLY B:550 , ARG B:553BINDING SITE FOR RESIDUE CL A 6
05AC5SOFTWAREMG A:3 , TRP A:401 , LEU A:433 , ASN A:438 , PRO A:439 , GLY A:461 , SER A:462 , GLY A:463 , LYS A:464 , THR A:465 , SER A:466 , GLN A:493 , MET B:498 , ARG B:508BINDING SITE FOR RESIDUE ATP A 1
06AC6SOFTWAREMG B:4 , TRP B:401 , GLY B:461 , SER B:462 , GLY B:463 , LYS B:464 , THR B:465 , SER B:466 , GLN B:493BINDING SITE FOR RESIDUE ATP B 2
07AC7SOFTWARELEU A:541 , GLY A:542 , GLY A:545 , VAL A:546 , THR A:547BINDING SITE FOR RESIDUE ACY A 7
08AC8SOFTWARELEU B:541 , GLY B:542 , GLY B:545 , VAL B:546 , THR B:547BINDING SITE FOR RESIDUE ACY B 8
09AC9SOFTWARELYS A:532 , SER A:549 , LYS B:532 , GLN B:552BINDING SITE FOR RESIDUE ACY A 9
10BC1SOFTWAREGLY B:451 , ALA B:596BINDING SITE FOR RESIDUE ACY B 10

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ABC_TRANSPORTER_1PS00211 ABC transporters family signature.CFTR_MOUSE548-562
 
  2A:548-562
B:548-562
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ABC_TRANSPORTER_1PS00211 ABC transporters family signature.CFTR_MOUSE548-562
 
  1A:548-562
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ABC_TRANSPORTER_1PS00211 ABC transporters family signature.CFTR_MOUSE548-562
 
  1-
B:548-562

(-) Exons   (0, 0)

(no "Exon" information available for 1XFA)

(-) 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:264
 aligned with CFTR_MOUSE | P26361 from UniProtKB/Swiss-Prot  Length:1476

    Alignment length:281
                                   399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669 
           CFTR_MOUSE   390 TGIIMENVTAFWEEGFGELLEKVQQSNGDRKHSSDENNVSFSHLCLVGNPVLKNINLNIEKGEMLAITGSTGSGKTSLLMLILGELEASEGIIKHSGRVSFCSQFSWIMPGTIKENIIFGVSYDEYRYKSVVKACQLQQDITKFAEQDNTVLGEGGVTLSGGQRARISLARAVYKDADLYLLDSPFGYLDVFTEEQVFESCVCKLMANKTRILVTSKMEHLRKADKILILHQGSSYFYGTFSELQSLRPDFSSKLMGYDTFDQFTEERRSSILTETLRRFS 670
               SCOP domains d1xfaa_ A: Cystic fibr                 osis transmembrane conductance regulator, CFTR, nucleotide-binding domain                                                                                                                                                                          SCOP domains
               CATH domains 1xfaA00 A:390-670 P-lo                 op containing nucleotide triphosphate hydrolases                                                                                                                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee...hhhhhhh.-----------------hhhhhhhhh.eeeeeeeeee....eeeeee....hhhhhhhhhh......eeeeee...eeee........eehhhhhhh....hhhhhhhhhhhh.hhhhhh...hhhh.ee.......hhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhh......eeeee..hhhhhhh..eeeeee..eeeeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------ABC_TRANSPORTER------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xfa A 390 TGIIMENVTAFWEEGFGELLEK-----------------SFSHLCLVGNPVLKNINLNIEKGEMLAITGSTGSGKTSLLMLILGELEASEGIIKHSGRVSFCSQFSWIMPGTIKENIIRGVSYDEYRYKSVVKACQLQQDITKFAEQDNTVLGEGGVTLSGGQRARISLARAVYKDADLYLLDSPFGYLDVFTEEQVFESCVCKLMANKTRILVTSKMEHLRKADKILILHQGSSYFYGTFSELQSLRPDFSSKLMGYDTFDQFTEERRSSILTETLRRFS 670
                                   399       409 |       -       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669 
                                               411               429                                                                                                                                                                                                                                                 

Chain B from PDB  Type:PROTEIN  Length:264
 aligned with CFTR_MOUSE | P26361 from UniProtKB/Swiss-Prot  Length:1476

    Alignment length:281
                                   399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669 
           CFTR_MOUSE   390 TGIIMENVTAFWEEGFGELLEKVQQSNGDRKHSSDENNVSFSHLCLVGNPVLKNINLNIEKGEMLAITGSTGSGKTSLLMLILGELEASEGIIKHSGRVSFCSQFSWIMPGTIKENIIFGVSYDEYRYKSVVKACQLQQDITKFAEQDNTVLGEGGVTLSGGQRARISLARAVYKDADLYLLDSPFGYLDVFTEEQVFESCVCKLMANKTRILVTSKMEHLRKADKILILHQGSSYFYGTFSELQSLRPDFSSKLMGYDTFDQFTEERRSSILTETLRRFS 670
               SCOP domains d1xfab_ B: Cystic fibr                 osis transmembrane conductance regulator, CFTR, nucleotide-binding domain                                                                                                                                                                          SCOP domains
               CATH domains 1xfaB00 B:390-670 P-lo                 op containing nucleotide triphosphate hydrolases                                                                                                                                                                                                   CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------ABC_tran-1xfaB01 B:465-576                                                                                      --------------------------------------------------------------CFTR_R-1xfaB03 B:639-670         Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------ABC_tran-1xfaB02 B:465-576                                                                                      --------------------------------------------------------------CFTR_R-1xfaB04 B:639-670         Pfam domains (2)
         Sec.struct. author ..eeeeeeeee...hhhhhh..-----------------hhhhhhhhh.eeeeeeeeee....eeeeee....hhhhhhhhhh......eeeeee...eeee........eehhhhhhh....hhhhhhhhhhhh.hhhhhh...hhhh.eehhhhh..hhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhh......eeeee..hhhhhhh..eeeeee..eeeeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------ABC_TRANSPORTER------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xfa B 390 TGIIMENVTAFWEEGFGELLEK-----------------SFSHLCLVGNPVLKNINLNIEKGEMLAITGSTGSGKTSLLMLILGELEASEGIIKHSGRVSFCSQFSWIMPGTIKENIIRGVSYDEYRYKSVVKACQLQQDITKFAEQDNTVLGEGGVTLSGGQRARISLARAVYKDADLYLLDSPFGYLDVFTEEQVFESCVCKLMANKTRILVTSKMEHLRKADKILILHQGSSYFYGTFSELQSLRPDFSSKLMGYDTFDQFTEERRSSILTETLRRFS 670
                                   399       409 |       -       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669 
                                               411               429                                                                                                                                                                                                                                                 

   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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 4)

Asymmetric Unit

(-) Gene Ontology  (46, 46)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CFTR_MOUSE | P26361)
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:0030165    PDZ domain binding    Interacting selectively and non-covalently with a PDZ domain of a protein, a domain found in diverse signaling proteins.
    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:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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:0006695    cholesterol biosynthetic process    The chemical reactions and pathways resulting in the formation of cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones.
    GO:0030301    cholesterol transport    The directed movement of cholesterol, cholest-5-en-3-beta-ol, 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:1902161    positive regulation of cyclic nucleotide-gated ion channel activity    Any process that activates or increases the frequency, rate or extent of cyclic nucleotide-gated ion channel activity.
    GO:0045921    positive regulation of exocytosis    Any process that activates or increases the frequency, rate or extent of exocytosis.
    GO:0035774    positive regulation of insulin secretion involved in cellular response to glucose stimulus    Any process that increases the frequency, rate or extent of the regulated release of insulin that contributes to the response of a cell to glucose.
    GO:1902943    positive regulation of voltage-gated chloride channel activity    Any process that activates or increases the frequency, rate or extent of voltage-gated chloride channel activity.
    GO:0003254    regulation of membrane depolarization    Any process that modulates the rate, frequency or extent of membrane depolarization. Membrane depolarization is the process in which membrane potential changes in the depolarizing direction from the resting potential, usually from negative to positive.
    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.
    GO:0006904    vesicle docking involved in exocytosis    The initial attachment of a vesicle membrane to a target membrane, mediated by proteins protruding from the membrane of the vesicle and the target membrane, that contributes to exocytosis.
cellular component
    GO:0016324    apical plasma membrane    The region of the plasma membrane located at the apical end of the cell.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0034707    chloride channel complex    An ion channel complex through which chloride ions pass.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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:0031205    endoplasmic reticulum Sec complex    An endoplasmic reticulum membrane-associated complex involved in the translocation of proteins that are targeted to the ER. In yeast, this complex consists of two subcomplexes, namely, the Sec61 complex and the Sec62/Sec63 complex.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
    GO:0055037    recycling endosome    An organelle consisting of a network of tubules that functions in targeting molecules, such as receptors transporters and lipids, to the plasma membrane.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CFTR_MOUSE | P263611q3h 1r0w 1r0x 1r0y 1r0z 1r10 1xf9 3si7

(-) Related Entries Specified in the PDB File

1xf9