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(-) Description

Title :  CALCIUM-BOUND LAMININ G LIKE DOMAIN 3 FROM HUMAN PERLECAN
 
Authors :  B. Van Le, K. K. Kim
Date :  16 Jun 11  (Deposition) - 14 Dec 11  (Release) - 14 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Actin Disassambly Activity, Integrin Alpha 2 Beta 1, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Van Le, H. Kim, J. Choi, J. H. Kim, M. J. Hahn, C. Lee, K. K. Kim, H. Y. Hwang
Crystal Structure Of The Lg3 Domain Of Endorepellin, An Angiogenesis Inhibitor.
J. Mol. Biol. V. 414 231 2011
PubMed-ID: 21996443  |  Reference-DOI: 10.1016/J.JMB.2011.09.048

(-) Compounds

Molecule 1 - LG3 PEPTIDE
    ChainsA
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymLAMININ-G LIKE DOMAIN 3, HSPG2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:62 , LEU A:79 , ALA A:129 , ASN A:131 , HOH A:216BINDING SITE FOR RESIDUE CA A 196

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:159 -A:193

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:27 -Pro A:28
2Ala A:172 -Pro A:173

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_047995S4331NPGBM_HUMANPolymorphism3736360AS135N

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3SH5)

(-) Exons   (0, 0)

(no "Exon" information available for 3SH5)

(-) Sequences/Alignments

Asymmetric/Biological 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:183
 aligned with PGBM_HUMAN | P98160 from UniProtKB/Swiss-Prot  Length:4391

    Alignment length:189
                                  4212      4222      4232      4242      4252      4262      4272      4282      4292      4302      4312      4322      4332      4342      4352      4362      4372      4382         
          PGBM_HUMAN   4203 GAYFHDDGFLAFPGHVFSRSLPEVPETIELEVRTSTASGLLLWQGVEVGEAGQGKDFISLGLQDGHLVFRYQLGSGEARLVSEDPINDGEWHRVTALREGRRGSIQVDGEELVSGRSPGPNVAVNAKGSVYIGGAPDVATLTGGRFSSGITGCVKNLVLHSARPGAPPPQPLDLQHRAQAGANTRPCPS 4391
               SCOP domains d3sh5a_ A: automated matches                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeehhhhhh.......eeeeeeeee....eeeeeee..------...eeeeeee..eeeeeee....eeeee..........eeeeeeee..eeeeee.....eeee.............eee....hhhhhh.........eeeeeeeee...................eeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------N------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3sh5 A    7 GAYFHDDGFLAFPGHVFSRSLPEVPETIELEVRTSTASGLLLWQGVE------GKDFISLGLQDGHLVFRYQLGSGEARLVSEDPINDGEWHRVTALREGRRGSIQVDGEELVSGRSPGPNVAVNAKGSVYIGGAPDVATLTGGRFSSGITGCVKNLVLHSARPGAPPPQPLDLQHRAQAGANTRPCPS  195
                                    16        26        36        46      |  -   |    66        76        86        96       106       116       126       136       146       156       166       176       186         
                                                                         53     60                                                                                                                                       

   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)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3SH5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SH5)

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PGBM_HUMAN | P98160)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0044267    cellular protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
    GO:0022617    extracellular matrix disassembly    A process that results in the breakdown of the extracellular matrix.
    GO:0030198    extracellular matrix organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
    GO:0006024    glycosaminoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of glycosaminoglycans, any of a group of polysaccharides that contain amino sugars.
    GO:0006027    glycosaminoglycan catabolic process    The chemical reactions and pathways resulting in the breakdown of glycosaminoglycans, any one of a group of polysaccharides that contain amino sugars.
    GO:0030203    glycosaminoglycan metabolic process    The chemical reactions and pathways involving glycosaminoglycans, any one of a group of polysaccharides that contain amino sugars. Formerly known as mucopolysaccharides, they include hyaluronic acid and chondroitin, which provide lubrication in joints and form part of the matrix of cartilage. The three-dimensional structure of these molecules enables them to trap water, which forms a gel and gives glycosaminoglycans their elastic properties.
    GO:0042157    lipoprotein metabolic process    The chemical reactions and pathways involving any conjugated, water-soluble protein in which the covalently attached nonprotein group consists of a lipid or lipids.
    GO:0001523    retinoid metabolic process    The chemical reactions and pathways involving retinoids, any member of a class of isoprenoids that contain or are derived from four prenyl groups linked head-to-tail. Retinoids include retinol and retinal and structurally similar natural derivatives or synthetic compounds, but need not have vitamin A activity.
cellular component
    GO:0005796    Golgi lumen    The volume enclosed by the membranes of any cisterna or subcompartment of the Golgi apparatus, including the cis- and trans-Golgi networks.
    GO:0005604    basement membrane    A thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers.
    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:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    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: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:0043202    lysosomal lumen    The volume enclosed within the lysosomal membrane.
    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:0005578    proteinaceous extracellular matrix    A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PGBM_HUMAN | P981603sh4

(-) Related Entries Specified in the PDB File

3sh4