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(-) Description

Title :  HUMAN POLY(ADP-RIBOSE) GLYCOHYDROLASE IN COMPLEX WITH SYNTHETIC DIMERIC ADP-RIBOSE
 
Authors :  M. J. Lambrecht, M. Brichacek, E. Barkauskaite, A. Ariza, I. Ahel, P. J. Hergenrother
Date :  09 Jul 15  (Deposition) - 22 Jul 15  (Release) - 22 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Parg, Adp-Ribose (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. J. Lambrecht, M. Brichacek, E. Barkauskaite, A. Ariza, I. Ahel, P. J. Hergenrother
Synthesis Of Dimeric Adp-Ribose And Its Structure With Human Poly(Adp-Ribose) Glycohydrolase.
J. Am. Chem. Soc. V. 137 3558 2015
PubMed-ID: 25706250  |  Reference-DOI: 10.1021/JA512528P

(-) Compounds

Molecule 1 - POLY(ADP-RIBOSE) GLYCOHYDROLASE
    ChainsA
    EC Number3.2.1.143
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantROSETTA PLYSS
    Expression System Vector TypePLASMID
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 27)

Asymmetric/Biological Unit (5, 27)
No.NameCountTypeFull Name
1AR62Ligand/Ion[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE
2BME1Ligand/IonBETA-MERCAPTOETHANOL
3GOL11Ligand/IonGLYCEROL
4PPI6Ligand/IonPROPANOIC ACID
5SO47Ligand/IonSULFATE ION

(-) Sites  (26, 26)

Asymmetric Unit (26, 26)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:575 , CYS A:603 , PRO A:673 , HOH A:2212BINDING SITE FOR RESIDUE BME A1966
02AC2SOFTWAREILE A:484 , ARG A:485 , VAL A:486 , ASP A:487 , PHE A:498 , HOH A:2041BINDING SITE FOR RESIDUE SO4 A1967
03AC3SOFTWARELYS A:567 , PRO A:838 , ARG A:842 , HOH A:2356 , HOH A:2417BINDING SITE FOR RESIDUE SO4 A1968
04AC4SOFTWAREALA A:750 , AR6 A:1965BINDING SITE FOR RESIDUE SO4 A1969
05AC5SOFTWAREGLU A:459 , MET A:461 , ARG A:462 , ARG A:466BINDING SITE FOR RESIDUE SO4 A1970
06AC6SOFTWAREGLU A:839 , LYS A:840 , ARG A:843BINDING SITE FOR RESIDUE SO4 A1971
07AC7SOFTWARETYR A:564 , ARG A:644 , ASN A:646 , ARG A:941 , HOH A:2127 , HOH A:2186BINDING SITE FOR RESIDUE SO4 A1972
08AC8SOFTWARETRP A:506 , ARG A:644BINDING SITE FOR RESIDUE SO4 A1973
09AC9SOFTWAREGLU A:727 , GLN A:735 , ARG A:758 , ASN A:762 , GLN A:788 , SER A:809 , HOH A:2268 , HOH A:2275 , HOH A:2314 , HOH A:2331BINDING SITE FOR RESIDUE GOL A1974
10BC1SOFTWAREGLU A:709 , CYS A:711 , GLU A:712 , THR A:924 , ASP A:927 , LYS A:930 , HOH A:2418BINDING SITE FOR RESIDUE GOL A1975
11BC2SOFTWAREASN A:869 , CYS A:872 , ASP A:904 , AR6 A:1964 , HOH A:2378BINDING SITE FOR RESIDUE GOL A1976
12BC3SOFTWAREALA A:796 , GLU A:797 , AR6 A:1965 , HOH A:2325BINDING SITE FOR RESIDUE GOL A1977
13BC4SOFTWAREHIS A:828 , PHE A:829 , ARG A:830 , ARG A:831 , ASP A:834 , LYS A:840 , HOH A:2419BINDING SITE FOR RESIDUE GOL A1978
14BC5SOFTWAREARG A:685 , ALA A:689 , GLU A:787BINDING SITE FOR RESIDUE GOL A1979
15BC6SOFTWAREASN A:508 , LEU A:614 , GLU A:652 , HOH A:2075 , HOH A:2200 , HOH A:2420BINDING SITE FOR RESIDUE GOL A1980
16BC7SOFTWAREASN A:740 , HIS A:828 , PHE A:875 , AR6 A:1965 , HOH A:2286 , HOH A:2421BINDING SITE FOR RESIDUE GOL A1981
17BC8SOFTWAREGLU A:585 , LEU A:589 , HOH A:2220BINDING SITE FOR RESIDUE GOL A1982
18BC9SOFTWAREHIS A:501 , TYR A:502 , PRO A:605 , ASN A:606 , PPI A:1987 , HOH A:2062BINDING SITE FOR RESIDUE GOL A1983
19CC1SOFTWAREGLY A:492 , GLN A:551 , LYS A:554 , ALA A:690 , HOH A:2113BINDING SITE FOR RESIDUE GOL A1984
20CC2SOFTWARETYR A:521 , ARG A:535 , TYR A:560 , ASN A:561 , VAL A:562 , HOH A:2125 , HOH A:2195BINDING SITE FOR RESIDUE PPI A1985
21CC3SOFTWARELEU A:471 , ARG A:816 , HOH A:2235 , HOH A:2313BINDING SITE FOR RESIDUE PPI A1986
22CC4SOFTWARECYS A:515 , GLU A:517 , GOL A:1983 , HOH A:2092BINDING SITE FOR RESIDUE PPI A1987
23CC5SOFTWAREGLY A:724 , PPI A:1990 , HOH A:2264BINDING SITE FOR RESIDUE PPI A1988
24CC6SOFTWARESER A:655 , ARG A:741 , HOH A:2199BINDING SITE FOR RESIDUE PPI A1989
25CC7SOFTWARETHR A:725 , TYR A:792 , GLY A:794 , PPI A:1988 , HOH A:2318 , HOH A:2323BINDING SITE FOR RESIDUE PPI A1990
26CC8SOFTWAREARG A:663 , ILE A:726 , GLU A:727 , PHE A:738 , ASN A:740 , GLY A:745 , SER A:749 , ALA A:750 , GLY A:751 , LEU A:752 , VAL A:753 , GLN A:754 , GLU A:755 , ASN A:756 , TYR A:795 , ASN A:869 , GLY A:871 , CYS A:872 , GLY A:873 , ALA A:874 , PHE A:875 , PHE A:902 , SO4 A:1969 , GOL A:1976 , GOL A:1977 , GOL A:1981 , HOH A:2284 , HOH A:2285 , HOH A:2288 , HOH A:2320 , HOH A:2325 , HOH A:2326 , HOH A:2327 , HOH A:2365 , HOH A:2416BINDING SITE FOR RESIDUES AR6 A1964 AND AR6 A1965

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A7R)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Met A:464 -Pro A:465
2Phe A:498 -Pro A:499

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A7R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A7R)

(-) Exons   (0, 0)

(no "Exon" information available for 5A7R)

(-) 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:506
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhhh..................eee..hhhhh..............................ee...eehhhhhhhhhh....hhhhhhhhhhhhhhhhh....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeeeehhhhhhhhhhhhh.....................hhhhhh....hhhhhhhhhhhhhhhhhhh....eeeeeeee.....hhhhh......eeee...hhhhhh...eeeeee....hhhhhh...hhhhhhhhhhhhhhhhhhhh......eeeeee.....eeee.hhhhheeeee...............eeeeee.....hhhhhhhhhhhhhhhhhhhhhhh....hhhhh..eeee.........hhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a7r A 450 DKKWLGTPIEEMRRMPRCGIRLPLLRPSANHTVTIRVDLLRAGEVPKPFPTHYKDLWDNKHVKMPCSEQNLYPVAGSRWELIQTALLNKFTRPQNLKDAILKYNVAYSKKWDFTALIDFWDKVLEEAEAQHLYQSILPDMVKIALCLPNICTQPIPLLAAAMNHSITMSQEQIASLLANAFFCTFPRRNAKMKSEYSSYPDINFNRLFEGRSSRKPEKLKTLFCYFRRVTAAAPTGLVTFTRQSLEDFPEWERCEKPLTRLHVTYEGTIEENGQGMLQVDFANRFVGGGVTSAGLVQENIRFLINPELIISRLFTEVLDHNECLIITGTEQYSEYTGYAETYRWSRSHEDGSERDDWQRRCTEIVAIDALHFRRYLDQFVPEKMRRELNKAYCGFLRPGVSSENLSAVATGNWGCGAFGGDARLKALIQILAAAAAERDVVYFTFGDSELMRDIYSMHIFLTERKLTVGDVYKLLLRYYNEECRNCSTPGPDIKLYPFIYHAVESC 963
                                   459       469       479       489       499       509       519   ||  537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877       887       897       907       917       927       937       947       957      
                                                                                                   523|                                                                                                                                                                                                                                                                                                                                                                                                                                               
                                                                                                    532                                                                                                                                                                                                                                                                                                                                                                                                                                               

   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 5A7R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A7R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A7R)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        PARG_HUMAN | Q86W564a0d 4b1g 4b1h 4b1i 4b1j 5lhb

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