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(-)Theoretical Model
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Theoretical Model  (Jmol Viewer)

(-) Description

Title :  THEORETICAL MODEL OF THE HUMAN CD6 LIGAND ALCAM (ACTIVATED LEUKOCYTE-CELL ADHESION MOLECULE), N-TERMINAL RECEPTOR-BINDING DOMAIN
 
Authors :  J. Bajorath, M. A. Bowen, A. Aruffo
Date :  28 Nov 95  (Deposition) - 03 Apr 96  (Release) - 03 Apr 96  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A
Keywords :  Cell Adhesion Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Bajorath, M. A. Bowen, A. Aruffo
Molecular Model Of The N-Terminal Receptor-Binding Domain Of The Human Cd6 Ligand Alcam.
Protein Sci. V. 4 1644 1995
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CD6 LIGAND ALCAM
    ChainsA
    FragmentN-TERMINAL IMMUNOGLOBULIN-LIKE DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    SynonymACTIVATED LEUKOCYTE-CELL ADHESION MOLECULE

 Structural Features

(-) Chains, Units

  
Theoretical Model 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1KJC)

(-) SS Bonds  (1, 1)

Theoretical Model
No.Residues
1A:16 -A:86

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (3, 3)

Theoretical Model (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003061071bENSE00001938712chr3:105085753-105086325573CD166_HUMAN1-25250--
1.5ENST000003061075ENSE00001801902chr3:105238911-105239011101CD166_HUMAN25-58341A:1-3131
1.6aENST000003061076aENSE00001618848chr3:105243133-105243352220CD166_HUMAN59-132741A:32-10574
1.8ENST000003061078ENSE00001795232chr3:105250846-10525091065CD166_HUMAN132-153221A:105-1062
1.9bENST000003061079bENSE00001606575chr3:105252447-10525253488CD166_HUMAN154-183300--
1.10ENST0000030610710ENSE00001642057chr3:105253507-105253689183CD166_HUMAN183-244620--
1.11bENST0000030610711bENSE00001151830chr3:105258819-105258946128CD166_HUMAN244-286430--
1.12ENST0000030610712ENSE00001151824chr3:105260477-105260609133CD166_HUMAN287-331450--
1.13cENST0000030610713cENSE00001151818chr3:105264067-105264179113CD166_HUMAN331-368380--
1.14ENST0000030610714ENSE00001151814chr3:105265993-105266128136CD166_HUMAN369-414460--
1.15aENST0000030610715aENSE00001507276chr3:105266234-105266367134CD166_HUMAN414-458450--
1.16aENST0000030610716aENSE00001507275chr3:105268971-105269103133CD166_HUMAN459-503450--
1.17ENST0000030610717ENSE00001151795chr3:105270988-10527102639CD166_HUMAN503-516140--
1.18aENST0000030610718aENSE00001151787chr3:105271312-105271429118CD166_HUMAN516-555400--
1.19ENST0000030610719ENSE00001161717chr3:105290696-105290808113CD166_HUMAN555-583290--
1.20eENST0000030610720eENSE00001878770chr3:105293321-1052957442424CD166_HUMAN-00--

(-) 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 A from PDB  Type:PROTEIN  Length:106
 aligned with CD166_HUMAN | Q13740 from UniProtKB/Swiss-Prot  Length:583

    Alignment length:106
                                    37        47        57        67        77        87        97       107       117       127      
          CD166_HUMAN    28 WYTVNSAYGDTIIIPCRLDVPQNLMFGKWKYEKPDGSPVFIAFRSSTKKSVQYDDVPEYKDRLNLSENYTLSISNARISDEKRFVCMLVTEDNVFEAPTIVKVFKQ 133
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeee..........eeeee.....eee.eee....eee.......eeeee....eeeeee.........eeeeeeee..eeee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5  PDB: A:1-31          Exon 1.6a  PDB: A:32-105 UniProt: 59-132                                  - Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------1. Transcript 1 (2)
                 1kjc A   1 WYTVNSAYGDTIIIPCRLDVPQNLMFGKWKYEKPDGSPVFIAFRSSTKKSVQYDDVPEYKDRLNLSENYTLSISNARISDEKRFVCMLVTEDNVFEAPTIVKVFKQ 106
                                    10        20        30        40        50        60        70        80        90       100      

   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 1KJC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1KJC)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (27, 27)

Theoretical Model(hide GO term definitions)
Chain A   (CD166_HUMAN | Q13740)
molecular function
    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).
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
    GO:0002250    adaptive immune response    An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
    GO:0048846    axon extension involved in axon guidance    The long distance growth of a single cell process, that is involved in the migration of an axon growth cone, where the migration is directed to a specific target site by a combination of attractive and repulsive cues.
    GO:0007411    axon guidance    The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0007157    heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules    The attachment of an adhesion molecule in one cell to a nonidentical adhesion molecule in an adjacent cell.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0008045    motor neuron axon guidance    The process in which the migration of an axon growth cone of a motor neuron is directed to a specific target site in response to a combination of attractive and repulsive cues.
    GO:1990138    neuron projection extension    Long distance growth of a single neuron projection involved in cellular development. A neuron projection is a prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0031290    retinal ganglion cell axon guidance    The process in which the migration of an axon growth cone of a retinal ganglion cell (RGC) is directed to its target in the brain in response to a combination of attractive and repulsive cues.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0042101    T cell receptor complex    A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains.
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    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: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:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0001772    immunological synapse    An area of close contact between a lymphocyte (T-, B-, or natural killer cell) and a target cell formed through the clustering of particular signaling and adhesion molecules and their associated membrane rafts on both the lymphocyte and the target cell and facilitating activation of the lymphocyte, transfer of membrane from the target cell to the lymphocyte, and in some situations killing of the target cell through release of secretory granules and/or death-pathway ligand-receptor interaction.
    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:0005887    integral component of plasma membrane    The component of the plasma 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:0031226    intrinsic component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    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.

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 Related Entries

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

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        CD166_HUMAN | Q137405a2f

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