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(-) Description

Title :  EXPLORING THE SUBSTRATE AFFINITIES OF MMP-3, ADAM-9 AND ADAM-10 USING MOLECULAR MODELLING AND DYNAMICS SIMULATIONS
 
Authors :  S. Manzetti, D. R. Mcculloch, A. C. Herington
Date :  20 Jun 02  (Deposition) - 05 Jul 02  (Release) - 04 Apr 05  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,B  (2x)
Keywords :  Zn-Binding, Metalloprotease, Similar To Snake Venome Acutolysin-C, Adamalysin Fold, Dimeric, Substrate (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Manzetti, D. R. Mcculloch, A. C. Herington, D. Van Der Spoel
Modeling Of Enzyme-Substrate Complexes For The Metalloproteases Mmp-3, Adam-9 And Adam-10
Comput. Aided Des. V. 17 551 2003
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MELTRIN GAMMA
    ChainsA
    EC Number3.4.24.17
    FragmentCATALYTIC DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    SynonymA DISINTEGRIN AND METALLOPROTEINASE DOMAIN 9
 
Molecule 2 - EMPIRICAL SUBSTRATE
    ChainsB
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  
Theoretical Model (2x)

Summary Information (see also Sequences/Alignments below)

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

Theoretical Model (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (0, 0)

(no "Site" information available for 1M1V)

(-) SS Bonds  (3, 3)

Theoretical Model
No.Residues
1A:116 -A:195
2A:157 -A:179
3A:159 -A:164

(-) Cis Peptide Bonds  (6, 11)

Theoretical Model
No.ModelResidues
11, 2Gly A:104 -Gly A:105
21, 2Asp A:156 -Cys A:157
31, 2Met A:166 -Asn A:167
41, 2Gly A:169 -Ala A:170
51, 2Phe A:176 -Ser A:177
62Ala A:170 -Ser A:171

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1M1V)

(-) PROSITE Motifs  (2, 2)

Theoretical Model (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADAM_MEPROPS50215 ADAM type metalloprotease domain profile.ADAM9_HUMAN212-406  1A:6-198
2ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.ADAM9_HUMAN344-353  1A:138-147

(-) Exons   (0, 0)

(no "Exon" information available for 1M1V)

(-) 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:197
 aligned with ADAM9_HUMAN | Q13443 from UniProtKB/Swiss-Prot  Length:819

    Alignment length:197
                                   217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       
          ADAM9_HUMAN   208 LPQTRYVELFIVVDKERYDMMGRNQTAVREEMILLANYLDSMYIMLNIRIVLVGLEIWTNGNLINIVGGAGDVLGNFVQWREKFLITRRRHDSAQLVLKKGFGGTAGMAFVGTVCSRSHAGGINVFGQITVETFASIVAHELGHNLGMNHDDGRDCSCGAKSCIMNSGASGSRNFSSCSAEDFEKLTLNKGGNCLLN 404
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeehhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee...........hhhhhhhhhhhhhhhh........eeeeee.....eeeeee..........eeeee.......hhhhhhhhhhhhhhh.............................hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----ADAM_MEPRO  PDB: A:6-198 UniProt: 212-406                                                                                                                                                         PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE--------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m1v A   2 LPQTRYVELFIVVDKERYDMMGRNQTAVREEMILLANYLDSMYIMLNIRIVLVGLEIWTNGNLINIVGGAGDVLGNFVQWREKFLITRRRHDSAQLVLKKGFGGTAGMAFVGTVCSRSHAGGINVFGQITVETFASIVAHELGHNLGMNHDDGRDCSCGAKSCIMNSGASGSRNFSSCSAEDFEKLTLNKGGNCLLN 198
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       

Chain B from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ..eeeee. Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 1m1v B   1 AALYLVCG   8

   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 1M1V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1M1V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1M1V)

(-) Gene Ontology  (44, 44)

Theoretical Model(hide GO term definitions)
Chain A   (ADAM9_HUMAN | Q13443)
molecular function
    GO:0017124    SH3 domain binding    Interacting selectively and non-covalently with a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins.
    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:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0005178    integrin binding    Interacting selectively and non-covalently with an integrin.
    GO:0043236    laminin binding    Interacting selectively and non-covalently with laminins, glycoproteins that are major constituents of the basement membrane of cells.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004222    metalloendopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    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:0005080    protein kinase C binding    Interacting selectively and non-covalently with protein kinase C.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0051088    PMA-inducible membrane protein ectodomain proteolysis    The proteolytic cleavage of transmembrane proteins and release of their ectodomain that occurs after induction by phorbol-12-myristate-13-acetate (PMA), a protein kinase C agonist.
    GO:0000186    activation of MAPKK activity    The initiation of the activity of the inactive enzyme MAP kinase kinase (MAPKK).
    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:0033627    cell adhesion mediated by integrin    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via an integrin, a heterodimeric adhesion receptor formed by the non-covalent association of particular alpha and beta subunits.
    GO:0033631    cell-cell adhesion mediated by integrin    The attachment of one cell to another cell via an integrin, a heterodimeric adhesion receptor formed by the non-covalent association of particular alpha and beta subunits.
    GO:0007160    cell-matrix adhesion    The binding of a cell to the extracellular matrix via adhesion molecules.
    GO:0071222    cellular response to lipopolysaccharide    Any process that results in a change in state or activity of a cell (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:0007229    integrin-mediated signaling pathway    A series of molecular signals initiated by the binding of extracellular ligand to an integrin on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0030216    keratinocyte differentiation    The process in which a relatively unspecialized cell acquires specialized features of a keratinocyte.
    GO:0006509    membrane protein ectodomain proteolysis    The proteolytic cleavage of transmembrane proteins and release of their ectodomain (extracellular domain).
    GO:0042117    monocyte activation    The change in morphology and behavior of a monocyte resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor.
    GO:0033630    positive regulation of cell adhesion mediated by integrin    Any process that activates or increases the frequency, rate, or extent of cell adhesion mediated by integrin.
    GO:0051549    positive regulation of keratinocyte migration    Any process that activates or increases the frequency, rate or extent of keratinocyte migration.
    GO:0034241    positive regulation of macrophage fusion    Any process that activates or increases the frequency, rate or extent of macrophage fusion.
    GO:0051044    positive regulation of membrane protein ectodomain proteolysis    Any process that activates or increases the frequency, rate or extent of membrane protein ectodomain peptidolysis.
    GO:0050714    positive regulation of protein secretion    Any process that activates or increases the frequency, rate or extent of the controlled release of a protein from a cell.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0051592    response to calcium ion    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 calcium ion stimulus.
    GO:0051384    response to glucocorticoid    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 glucocorticoid stimulus. Glucocorticoids are hormonal C21 corticosteroids synthesized from cholesterol with the ability to bind with the cortisol receptor and trigger similar effects. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects.
    GO:0042542    response to hydrogen peroxide    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 hydrogen peroxide (H2O2) stimulus.
    GO:0010042    response to manganese ion    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 manganese ion stimulus.
    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.
    GO:0007179    transforming growth factor beta receptor signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    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: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: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:0031233    intrinsic component of external side of plasma membrane    The component of a plasma membrane consisting of gene products and protein complexes that penetrate the external side of the plasma membrane only, either directly or via some covalently attached hydrophobic anchor.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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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