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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN SENESCENCE MARKER PROTEIN-30 (ZINC BOUND)
 
Authors :  S. Chakraborti, B. J. Bahnson
Date :  03 Feb 09  (Deposition) - 02 Feb 10  (Release) - 05 May 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.92
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Keywords :  Six Bladed Beta Propeller, Gluconolactonase, Organophosphate Hydrolase, Regucalcin, Zinc Bound, Alternative Splicing, Calcium, Cytoplasm, Phosphoprotein, Signaling Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Chakraborti, B. J. Bahnson
Crystal Structure Of Human Senescence Marker Protein 30: Insights Linking Structural, Enzymatic, And Physiological Functions .
Biochemistry V. 49 3436 2010
PubMed-ID: 20329768  |  Reference-DOI: 10.1021/BI9022297

(-) Compounds

Molecule 1 - REGUCALCIN
    ChainsB, A
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX4T3
    Expression System StrainBL21(DE3)RIL CODON PLUS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneRGN, SMP30
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRC, SENESCENCE MARKER PROTEIN 30, SMP-30

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)AB
Biological Unit 2 (1x)A 
Biological Unit 3 (1x) B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:18 , ASN A:154 , ASP A:204 , HOH A:315 , HOH A:326 , HOH A:356BINDING SITE FOR RESIDUE ZN A 300
2AC2SOFTWAREGLU B:18 , ASN B:154 , ASP B:204 , HOH B:344BINDING SITE FOR RESIDUE ZN B 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3G4H)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Pro B:124 -Ala B:125

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3G4H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3G4H)

(-) Exons   (0, 0)

(no "Exon" information available for 3G4H)

(-) Sequences/Alignments

Asymmetric 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:297
 aligned with RGN_HUMAN | Q15493 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:297
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       
            RGN_HUMAN     3 SIKIECVLPENCRCGESPVWEEVSNSLLFVDIPAKKVCRWDSFTKQVQRVTMDAPVSSVALRQSGGYVATIGTKFCALNWKEQSAVVLATVDNDKKNNRFNDGKVDPAGRYFAGTMAEETAPAVLERHQGALYSLFPDHHVKKYFDQVDISNGLDWSLDHKIFYYIDSLSYSVDAFDYDLQTGQISNRRSVYKLEKEEQIPDGMCIDAEGKLWVACYNGGRVIRLDPVTGKRLQTVKLPVDKTTSCCFGGKNYSEMYVTCARDGMDPEGLLRQPEAGGIFKITGLGVKGIAPYSYAG 299
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......eeeeeeehhh.eeeeee....eeeeee.....eeeee....eeeeee.....eeeee..eeeeee....eeeeeee.......eeeeeeee.....eeeeeee............eeeeee.....eeeeeeee..eeeeee.....eeeeee....eeeeeee......eeeeeeeee.hhhhheeeeeee.....eeeeee...eeeeee....eeeeeee.....eeeeeeehhhhheeeeee.....hhhhhhhh.....eeeee.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g4h A   3 SIKIECVLPENCRCGESPVWEEVSNSLLFVDIPAKKVCRWDSFTKQVQRVTMDAPVSSVALRQSGGYVATIGTKFCALNWKEQSAVVLATVDNDKKNNRFNDGKVDPAGRYFAGTMAEETAPAVLERHQGALYSLFPDHHVKKYFDQVDISNGLDWSLDHKIFYYIDSLSYSVDAFDYDLQTGQISNRRSVYKLEKEEQIPDGMCIDAEGKLWVACYNGGRVIRLDPVTGKRLQTVKLPVDKTTSCCFGGKNYSEMYVTCARDGMDPEGLLRQPEAGGIFKITGLGVKGIAPYSYAG 299
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       

Chain B from PDB  Type:PROTEIN  Length:297
 aligned with RGN_HUMAN | Q15493 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:297
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       
            RGN_HUMAN     3 SIKIECVLPENCRCGESPVWEEVSNSLLFVDIPAKKVCRWDSFTKQVQRVTMDAPVSSVALRQSGGYVATIGTKFCALNWKEQSAVVLATVDNDKKNNRFNDGKVDPAGRYFAGTMAEETAPAVLERHQGALYSLFPDHHVKKYFDQVDISNGLDWSLDHKIFYYIDSLSYSVDAFDYDLQTGQISNRRSVYKLEKEEQIPDGMCIDAEGKLWVACYNGGRVIRLDPVTGKRLQTVKLPVDKTTSCCFGGKNYSEMYVTCARDGMDPEGLLRQPEAGGIFKITGLGVKGIAPYSYAG 299
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......eeeeeee....eeeeee....eeeeee.....eeeee....eeeeee.....eeeee..eeeee......eeeeee.......eeeeeeee.....eeeeeee............eeeeee.....eeeeeeee..eeeeee.....eeeeee....eeeeeee......eeeeeeeee.hhhhheeeeeee.....eeeeee...eeeee......eeeeee.....eeeeeeehhhhheeeeee.....hhhhhh.......eeeee.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g4h B   3 SIKIECVLPENCRCGESPVWEEVSNSLLFVDIPAKKVCRWDSFTKQVQRVTMDAPVSSVALRQSGGYVATIGTKFCALNWKEQSAVVLATVDNDKKNNRFNDGKVDPAGRYFAGTMAEETAPAVLERHQGALYSLFPDHHVKKYFDQVDISNGLDWSLDHKIFYYIDSLSYSVDAFDYDLQTGQISNRRSVYKLEKEEQIPDGMCIDAEGKLWVACYNGGRVIRLDPVTGKRLQTVKLPVDKTTSCCFGGKNYSEMYVTCARDGMDPEGLLRQPEAGGIFKITGLGVKGIAPYSYAG 299
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       

   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 3G4H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3G4H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3G4H)

(-) Gene Ontology  (43, 43)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RGN_HUMAN | Q15493)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0030234    enzyme regulator activity    Binds to and modulates the activity of an enzyme.
    GO:0004341    gluconolactonase activity    Catalysis of the reaction: D-glucono-1,5-lactone + H2O = D-gluconate.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0019853    L-ascorbic acid biosynthetic process    The chemical reactions and pathways resulting in the formation of L-ascorbic acid; L-ascorbic acid ionizes to give L-ascorbate, (2R)-2-[(1S)-1,2-dihydroxyethyl]-4-hydroxy-5-oxo-2,5-dihydrofuran-3-olate, which is required as a cofactor in the oxidation of prolyl residues to hydroxyprolyl, and other reactions.
    GO:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    GO:0006874    cellular calcium ion homeostasis    Any process involved in the maintenance of an internal steady state of calcium ions at the level of a cell.
    GO:0001822    kidney development    The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine.
    GO:0001889    liver development    The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes.
    GO:0097421    liver regeneration    The regrowth of lost or destroyed liver.
    GO:2000279    negative regulation of DNA biosynthetic process    Any process that stops, prevents or reduces the frequency, rate or extent of DNA biosynthetic process.
    GO:1903625    negative regulation of DNA catabolic process    Any process that stops, prevents or reduces the frequency, rate or extent of DNA catabolic process.
    GO:0034260    negative regulation of GTPase activity    Any process that stops or reduces the rate of GTP hydrolysis by a GTPase.
    GO:1902679    negative regulation of RNA biosynthetic process    Any process that stops, prevents or reduces the frequency, rate or extent of RNA biosynthetic process.
    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.
    GO:1903011    negative regulation of bone development    Any process that stops, prevents or reduces the frequency, rate or extent of bone development.
    GO:1903611    negative regulation of calcium-dependent ATPase activity    Any process that stops, prevents or reduces the frequency, rate or extent of calcium-dependent ATPase activity.
    GO:0051344    negative regulation of cyclic-nucleotide phosphodiesterase activity    Any process that stops or reduces the rate of cyclic nucleotide phosphodiesterase activity, the catalysis of the reaction: nucleotide 3',5'-cyclic phosphate + H2O = nucleotide 5'-phosphate.
    GO:0050680    negative regulation of epithelial cell proliferation    Any process that stops, prevents or reduces the rate or extent of epithelial cell proliferation.
    GO:1901318    negative regulation of flagellated sperm motility    Any process that stops, prevents or reduces the frequency, rate or extent of flagellated sperm motility.
    GO:1903634    negative regulation of leucine-tRNA ligase activity    Any process that stops, prevents or reduces the frequency, rate or extent of leucine-tRNA ligase activity.
    GO:0045019    negative regulation of nitric oxide biosynthetic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of nitric oxide.
    GO:0032515    negative regulation of phosphoprotein phosphatase activity    Any process that stops or reduces the activity of a phosphoprotein phosphatase.
    GO:0006469    negative regulation of protein kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity.
    GO:0001933    negative regulation of protein phosphorylation    Any process that stops, prevents or reduces the rate of addition of phosphate groups to amino acids within a protein.
    GO:0032781    positive regulation of ATPase activity    Any process that activates or increases the rate of ATP hydrolysis by an ATPase.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:1901896    positive regulation of calcium-transporting ATPase activity    Any process that activates or increases the frequency, rate or extent of calcium-transporting ATPase activity.
    GO:1903629    positive regulation of dUTP diphosphatase activity    Any process that activates or increases the frequency, rate or extent of dUTP diphosphatase activity.
    GO:0045723    positive regulation of fatty acid biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of fatty acids.
    GO:0010907    positive regulation of glucose metabolic process    Any process that increases the rate, frequency or extent of glucose metabolism. Glucose metabolic processes are the chemical reactions and pathways involving glucose, the aldohexose gluco-hexose.
    GO:0010922    positive regulation of phosphatase activity    Any process that increases the rate or frequency of phosphatase activity. Phosphatases catalyze the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:1903052    positive regulation of proteolysis involved in cellular protein catabolic process    Any process that activates or increases the frequency, rate or extent of proteolysis involved in cellular protein catabolic process.
    GO:1901671    positive regulation of superoxide dismutase activity    Any process that activates or increases the frequency, rate or extent of superoxide dismutase activity.
    GO:0010867    positive regulation of triglyceride biosynthetic process    Any process that increases the rate, frequency, or extent of triglyceride biosynthesis. Triglyceride biosynthesis is the collection of chemical reactions and pathways resulting in the formation of triglyceride, any triester of glycerol.
    GO:0050848    regulation of calcium-mediated signaling    Any process that modulates the frequency, rate or extent of calcium-mediated signaling, the process in which a cell uses calcium ions to convert an extracellular signal into a response.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RGN_HUMAN | Q154933g4e 4gnb 4gnc

(-) Related Entries Specified in the PDB File

3g4e SAME PROTEIN COMPLEXED WITH CALCIUM