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(-) Description

Authors :  J. Wuerges, S. Geremia, L. Randaccio
Date :  21 Apr 06  (Deposition) - 13 Feb 07  (Release) - 13 Feb 07  (Revision)
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  W#,X
#:   chains that contain no standard or modified protein/DNA/RNA residue)
Keywords :  Ion Transport, Disease Mutation, Cobalt Transport, Comparative Model, Vitamin B12 Transport Protein, Cobalt, Transport, Polymorphism, Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  J. Wuerges, S. Geremia, L. Randaccio
Structural Study On Ligand Specificity Of Human Vitamin B12 Transporters.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds


 Structural Features

(-) Chains, Units

Theoretical Model 
#:   chains that contain no standard or modified protein/DNA/RNA residue)

Summary Information (see also Sequences/Alignments below)

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

Theoretical Model (1, 1)
No.NameCountTypeFull Name

(-) Sites  (0, 0)

(no "Site" information available for 2CKT)

(-) SS Bonds  (3, 3)

Theoretical Model
1X:8 -X:228
2X:85 -X:270
3X:125 -X:164

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Theoretical Model (4, 4)
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
2UniProtVAR_022743S46LIF_HUMANDisease (IFD)121434322XS28L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Theoretical Model (1, 1)
1COBALAMIN_BINDINGPS00468 Eukaryotic cobalamin-binding proteins signature.IF_HUMAN169-182  1X:151-164

(-) Exons   (9, 9)

Theoretical Model (9, 9)
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength

(-) Sequences/Alignments

Theoretical Model
   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 X from PDB  Type:PROTEIN  Length:399
 aligned with IF_HUMAN | P27352 from UniProtKB/Swiss-Prot  Length:417

    Alignment length:399
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhh.........hhhhhhhh......hhhhhhhhhhh......hhhhhhhhhhhhhhh.......hhhhhhhhhhhh..........hhhhhhhhhhhhhhh.......hhhhhhhh......hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh..hhhhhhhh.......................eeeeeeeeee.............eeeeeee...hhhhhh.........eeeeeee..eeeeeeee.eee....eeeeeeeee.eee............eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ----R----------------------L------------------R---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------COBALAMIN_BIND------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a----------------------------------------------------------Exon 1.3a  PDB: X:68-106               ----------------------------------------------Exon 1.4a  PDB: X:153-213 UniProt: 171-231                   Exon 1.5  PDB: X:214-273 UniProt: 232-291                   ------------------------------------------------------------------Exon 1.7a  PDB: X:340-380                ------------------- Transcript 1 (1)
           Transcript 1 (2) --------Exon 1.2  PDB: X:9-68 UniProt: 27-86                        -------------------------------------Exon 1.3c  PDB: X:106-153 UniProt: 124-171      -----------------------------------------------------------------------------------------------------------------------Exon 1.6a  PDB: X:273-340 UniProt: 291-358                          ---------------------------------------Exon 1.8b            Transcript 1 (2)
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390         

   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 2CKT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Theoretical Model(hide GO term definitions)
Chain X   (IF_HUMAN | P27352)
molecular function
    GO:0031419    cobalamin binding    Interacting selectively and non-covalently with cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.
biological process
    GO:0009235    cobalamin metabolic process    The chemical reactions and pathways involving cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.
    GO:0015889    cobalamin transport    The directed movement of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006824    cobalt ion transport    The directed movement of cobalt (Co) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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: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:0016324    apical plasma membrane    The region of the plasma membrane located at the apical end of the cell.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    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:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0043202    lysosomal lumen    The volume enclosed within the lysosomal membrane.
    GO:0005902    microvillus    Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells.


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 Related Entries

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

        IF_HUMAN | P273522pmv 3kq4

(-) Related Entries Specified in the PDB File

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