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

(-) Description

Title :  THEORETICAL MODEL OF E-SELECTIN, C-TYPE LECTIN DOMAIN, RESIDUES 1-120, CELL ADHESION MOLECULE
 
Authors :  J. Bajorath, R. Stenkamp, 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,_#
#:   chains that contain no standard or modified protein/DNA/RNA residue)
 
Keywords :  Cell Adhesion Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Bajorath, R. Stenkamp, A. Aruffo
Comparison Of A Protein Model With Its X-Ray Structure: The Ligand Binding Domain Of E-Selectin.
Bioconjug. Chem. V. 6 3 1995
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - E-SELECTIN
    ChainsA
    FragmentC-TYPE LECTIN DOMAIN,RESIDUES 1 - 120
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS

 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
1CA1Ligand/IonCALCIUM ION

(-) Sites  (0, 0)

(no "Site" information available for 1KJA)

(-) SS Bonds  (2, 2)

Theoretical Model
No.Residues
1A:19 -A:117
2A:90 -A:109

(-) Cis Peptide Bonds  (1, 1)

Theoretical Model
No.Residues
1Glu A:80 -Pro A:81

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Theoretical Model (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_014301M31ILYAM2_HUMANPolymorphism3917408AM10I
2UniProtVAR_011790C130WLYAM2_HUMANPolymorphism5360AC109W

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

(-) PROSITE Motifs  (2, 2)

Theoretical Model (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.LYAM2_HUMAN111-138  1A:90-117
2EGF_3PS50026 EGF-like domain profile.LYAM2_HUMAN139-175  1A:118-120

(-) Exons   (2, 2)

Theoretical Model (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003333601bENSE00001950222chr1:169703203-16970311292LYAM2_HUMAN-00--
1.2aENST000003333602aENSE00001367867chr1:169702801-16970271785LYAM2_HUMAN1-13130--
1.3aENST000003333603aENSE00000814463chr1:169702139-169701756384LYAM2_HUMAN13-1411291A:1-120120
1.4aENST000003333604aENSE00000789645chr1:169701083-169700976108LYAM2_HUMAN141-177371A:120-1201
1.5ENST000003333605ENSE00000789644chr1:169699758-169699573186LYAM2_HUMAN177-239630--
1.6ENST000003333606ENSE00000451012chr1:169698814-169698629186LYAM2_HUMAN239-301630--
1.7ENST000003333607ENSE00000789642chr1:169698515-169698327189LYAM2_HUMAN301-364640--
1.8ENST000003333608ENSE00000789641chr1:169697387-169697199189LYAM2_HUMAN364-427640--
1.9ENST000003333609ENSE00000451027chr1:169697068-169696880189LYAM2_HUMAN427-490640--
1.10ENST0000033336010ENSE00000789639chr1:169696666-169696490177LYAM2_HUMAN490-549600--
1.11ENST0000033336011ENSE00000451043chr1:169695947-169695840108LYAM2_HUMAN549-585370--
1.12ENST0000033336012ENSE00000789637chr1:169695069-16969504822LYAM2_HUMAN585-59280--
1.13ENST0000033336013ENSE00000814464chr1:169694942-16969487073LYAM2_HUMAN592-610190--
1.14aENST0000033336014aENSE00000814465chr1:169693650-1696917821869LYAM2_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:120
 aligned with LYAM2_HUMAN | P16581 from UniProtKB/Swiss-Prot  Length:610

    Alignment length:120
                                    31        41        51        61        71        81        91       101       111       121       131       141
          LYAM2_HUMAN    22 WSYNTSTEAMTYDEASAYCQQRYTHLVAIQNKEEIEYLNSILSYSPSYYWIGIRKVNNVWVWVGTQKPLTEEAKNWAPGEPNNRQKDEDCVEIYIKREKDVGMWNDERCSKKKLALCYTA 141
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........hhhhhhhhhh..........hhhhhhhhhh.......eeeeeee....eee...........................eeeeee......eeeeee............. Sec.struct. author
                 SAPs(SNPs) ---------I--------------------------------------------------------------------------------------------------W----------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------C_TYPE_LECTIN_1             EGF PROSITE
           Transcript 1 (1) Exon 1.3a  PDB: A:1-120 UniProt: 13-141 [INCOMPLETE]                                                                     Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------------1 Transcript 1 (2)
                 1kja A   1 WSYNTSTEAMTYDEASAYCQQRYTHLVAIQNKEEIEYLNSILSYSPSYYWIGIRKVNNVWVWVGTQKPLTEEAKNWAPGEPNNRQKDEDCVEIYIKREKDVGMWNDERCSKKKLALCYTA 120
                                    10        20        30        40        50        60        70        80        90       100       110       120

   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 1KJA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (30, 30)

Theoretical Model(hide GO term definitions)
Chain A   (LYAM2_HUMAN | P16581)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0070492    oligosaccharide binding    Interacting selectively and non-covalently with any oligosaccharide, a molecule with between two and (about) 20 monosaccharide residues connected by glycosidic linkages.
    GO:0043274    phospholipase binding    Interacting selectively and non-covalently with any phospholipase, enzymes that catalyze of the hydrolysis of a glycerophospholipid.
    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:0033691    sialic acid binding    Interacting selectively and non-covalently with sialic acid, any of a variety of N- or O- substituted derivatives of neuraminic acid, a nine carbon monosaccharide. Sialic acids often occur in polysaccharides, glycoproteins, and glycolipids in animals and bacteria.
    GO:0004888    transmembrane signaling receptor activity    Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction.
biological process
    GO:0030029    actin filament-based process    Any cellular process that depends upon or alters the actin cytoskeleton, that part of the cytoskeleton comprising actin filaments and their associated proteins.
    GO:0007202    activation of phospholipase C activity    The initiation of the activity of the inactive enzyme phospolipase C as the result of a series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand.
    GO:0019722    calcium-mediated signaling    Any intracellular signal transduction in which the signal is passed on within the cell via calcium ions.
    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:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0007159    leukocyte cell-cell adhesion    The attachment of a leukocyte to another cell via adhesion molecules.
    GO:0050900    leukocyte migration    The movement of a leukocyte within or between different tissues and organs of the body.
    GO:0002523    leukocyte migration involved in inflammatory response    The movement of a leukocyte within or between different tissues and organs of the body contributing to an inflammatory response.
    GO:0050901    leukocyte tethering or rolling    Transient adhesive interactions between leukocytes and endothelial cells lining blood vessels. Carbohydrates on circulating leukocytes bind selectins on the vessel wall causing the leukocytes to slow down and roll along the inner surface of the vessel wall. During this rolling motion, transitory bonds are formed and broken between selectins and their ligands. Typically the first step in cellular extravasation (the movement of leukocytes out of the circulatory system, towards the site of tissue damage or infection).
    GO:0002092    positive regulation of receptor internalization    Any process that activates or increases the frequency, rate or extent of receptor internalization.
    GO:0050727    regulation of inflammatory response    Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents.
    GO:0070555    response to interleukin-1    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interleukin-1 stimulus.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0034612    response to tumor necrosis factor    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tumor necrosis factor stimulus.
cellular component
    GO:0005901    caveola    A membrane raft that forms small pit, depression, or invagination that communicates with the outside of a cell and extends inward, indenting the cytoplasm and the cell membrane. Examples include flask-shaped invaginations of the plasma membrane in adipocytes associated with caveolin proteins, and minute pits or incuppings of the cell membrane formed during pinocytosis. Caveolae may be pinched off to form free vesicles within the cytoplasm.
    GO:0005905    clathrin-coated pit    A part of the endomembrane system in the form of an invagination of a membrane upon which a clathrin coat forms, and that can be converted by vesicle budding into a clathrin-coated vesicle. Coated pits form on the plasma membrane, where they are involved in receptor-mediated selective transport of many proteins and other macromolecules across the cell membrane, in the trans-Golgi network, and on some endosomes.
    GO:0030863    cortical cytoskeleton    The portion of the cytoskeleton that lies just beneath the plasma membrane.
    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: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:0045121    membrane raft    Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    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

Theoretical Model
  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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 1kja)
 
  Cis Peptide Bonds
    Glu A:80 - Pro A:81   [ RasMol ]  
 

(-) 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
  1kja
    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
  LYAM2_HUMAN | P16581
    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
  LYAM2_HUMAN | P16581
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        LYAM2_HUMAN | P165811esl 1g1t 4c16 4csy

(-) Related Entries Specified in the PDB File

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