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(-) Description

Title :  STORAGE FUNCTION OF COMP:THE CRYSTAL STRUCTURE OF THE COILED-COIL DOMAIN IN COMPLEX WITH VITAMIN D3
 
Authors :  J. Stetefeld
Date :  07 Oct 02  (Deposition) - 28 Jan 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Pentameric Coiled-Coil Domain, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Ozbek, J. Engel, J. Stetefeld
Storage Function Of Cartilage Oligomeric Matrix Protein: The Crystal Structure Of The Coiled-Coil Domain In Complex With Vitamin D(3).
Embo J. V. 21 5960 2002
PubMed-ID: 12426368  |  Reference-DOI: 10.1093/EMBOJ/CDF628
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CARTILAGE OLIGOMERIC MATRIX PROTEIN
    ChainsA, B, C, D, E
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET3B
    Expression System StrainJM109-DE3
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 27-71
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1VDY2Ligand/Ion3-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:40 , LEU A:51 , LEU B:44 , VAL B:47 , LEU B:51 , LEU C:44 , LEU C:51 , THR D:40 , LEU D:44 , VAL D:47 , LEU D:51 , LEU E:44BINDING SITE FOR RESIDUE VDY D 1001
2AC2SOFTWAREILE A:58 , LEU A:61 , ALA A:70 , ILE B:58 , LEU B:61 , VAL B:65 , ILE C:58 , LEU C:61 , VAL C:65 , ALA C:70 , LEU D:61 , VAL D:65 , LEU E:61 , VAL E:65 , CYS E:68 , ALA E:70BINDING SITE FOR RESIDUE VDY A 1002

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:68 -E:71
2A:71 -B:68
3B:71 -C:68
4D:71 -E:68

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1MZ9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1MZ9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1MZ9)

(-) Exons   (0, 0)

(no "Exon" information available for 1MZ9)

(-) 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:45
 aligned with COMP_MOUSE | Q9R0G6 from UniProtKB/Swiss-Prot  Length:755

    Alignment length:71
                                    10        20        30        40        50        60        70 
            COMP_MOUSE    1 MGPTACVLVLALAILRATGQGQIPLGGDLAPQMLRELQETNAALQDVRELLRQQVKEITFLKNTVMECDAC 71
               SCOP domains d                          1mz9a_ A:                                    SCOP domains
               CATH domains 1                          mz9A00 A:27-71                               CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author .--------------------------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  1mz9 A 27 M--------------------------DLAPQMLRELQETNAALQDVRELLRQQVKEITFLKNTVMECDAC 71
                            |        -         -       |30        40        50        60        70 
                            |                         28                                           
                           27                                                                      

Chain B from PDB  Type:PROTEIN  Length:45
 aligned with COMP_MOUSE | Q9R0G6 from UniProtKB/Swiss-Prot  Length:755

    Alignment length:71
                                    10        20        30        40        50        60        70 
            COMP_MOUSE    1 MGPTACVLVLALAILRATGQGQIPLGGDLAPQMLRELQETNAALQDVRELLRQQVKEITFLKNTVMECDAC 71
               SCOP domains d                          1mz9b_ B:                                    SCOP domains
               CATH domains 1                          mz9B00 B:27-71                               CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author .--------------------------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  1mz9 B 27 M--------------------------DLAPQMLRELQETNAALQDVRELLRQQVKEITFLKNTVMECDAC 71
                            |        -         -       |30        40        50        60        70 
                           27                         28                                           

Chain C from PDB  Type:PROTEIN  Length:45
 aligned with COMP_MOUSE | Q9R0G6 from UniProtKB/Swiss-Prot  Length:755

    Alignment length:71
                                    10        20        30        40        50        60        70 
            COMP_MOUSE    1 MGPTACVLVLALAILRATGQGQIPLGGDLAPQMLRELQETNAALQDVRELLRQQVKEITFLKNTVMECDAC 71
               SCOP domains d                          1mz9c_ C:                                    SCOP domains
               CATH domains 1                          mz9C00 C:27-71                               CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author .--------------------------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  1mz9 C 27 M--------------------------DLAPQMLRELQETNAALQDVRELLRQQVKEITFLKNTVMECDAC 71
                            |        -         -       |30        40        50        60        70 
                           27                         28                                           

Chain D from PDB  Type:PROTEIN  Length:45
 aligned with COMP_MOUSE | Q9R0G6 from UniProtKB/Swiss-Prot  Length:755

    Alignment length:71
                                    10        20        30        40        50        60        70 
            COMP_MOUSE    1 MGPTACVLVLALAILRATGQGQIPLGGDLAPQMLRELQETNAALQDVRELLRQQVKEITFLKNTVMECDAC 71
               SCOP domains d                          1mz9d_ D:                                    SCOP domains
               CATH domains 1                          mz9D00 D:27-71                               CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author .--------------------------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  1mz9 D 27 M--------------------------DLAPQMLRELQETNAALQDVRELLRQQVKEITFLKNTVMECDAC 71
                            |        -         -       |30        40        50        60        70 
                           27                         28                                           

Chain E from PDB  Type:PROTEIN  Length:45
 aligned with COMP_MOUSE | Q9R0G6 from UniProtKB/Swiss-Prot  Length:755

    Alignment length:71
                                    10        20        30        40        50        60        70 
            COMP_MOUSE    1 MGPTACVLVLALAILRATGQGQIPLGGDLAPQMLRELQETNAALQDVRELLRQQVKEITFLKNTVMECDAC 71
               SCOP domains d                          1mz9e_ E:                                    SCOP domains
               CATH domains 1                          mz9E00 E:27-71                               CATH domains
           Pfam domains (1) ---------------------------COMP-1mz9E01 E:28-71                         Pfam domains (1)
           Pfam domains (2) ---------------------------COMP-1mz9E02 E:28-71                         Pfam domains (2)
           Pfam domains (3) ---------------------------COMP-1mz9E03 E:28-71                         Pfam domains (3)
           Pfam domains (4) ---------------------------COMP-1mz9E04 E:28-71                         Pfam domains (4)
           Pfam domains (5) ---------------------------COMP-1mz9E05 E:28-71                         Pfam domains (5)
         Sec.struct. author .--------------------------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  1mz9 E 27 M--------------------------DLAPQMLRELQETNAALQDVRELLRQQVKEITFLKNTVMECDAC 71
                            |        -         -       |30        40        50        60        70 
                           27                         28                                           

   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, 5)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 5)

Asymmetric/Biological Unit

(-) Pfam Domains  (1, 5)

Asymmetric/Biological Unit
(-)
Family: COMP (2)
1aCOMP-1mz9E01E:28-71
1bCOMP-1mz9E02E:28-71
1cCOMP-1mz9E03E:28-71
1dCOMP-1mz9E04E:28-71
1eCOMP-1mz9E05E:28-71

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E   (COMP_MOUSE | Q9R0G6)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0005518    collagen binding    Interacting selectively and non-covalently with collagen, a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%).
    GO:0043395    heparan sulfate proteoglycan binding    Interacting selectively and non-covalently with a heparan sulfate proteoglycan, any proteoglycan containing heparan sulfate as the glycosaminoglycan carbohydrate unit.
    GO:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
    GO:0002020    protease binding    Interacting selectively and non-covalently with any protease or peptidase.
    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:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    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:0003417    growth plate cartilage development    The process whose specific outcome is the progression of the cartilage that will provide a scaffold for mineralization of endochondral bones as they elongate or grow.
    GO:0060173    limb development    The process whose specific outcome is the progression of a limb over time, from its formation to the mature structure. A limb is an appendage of an animal used for locomotion or grasping. Examples include legs, arms or some types of fin.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
cellular component
    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: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
        COMP_MOUSE | Q9R0G63v2n 3v2p 3v2q 3v2r

(-) Related Entries Specified in the PDB File

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