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(-) Description

Title :  POLYADPRIBOSYL GLYCOSIDASE IN COMPLEX WITH PDD00017262
 
Authors :  J. Tucker, E. Barkauskaite
Date :  10 Jul 16  (Deposition) - 12 Oct 16  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.23
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Competitive Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. I. James, K. M. Smith, A. M. Jordan, E. E. Fairweather, L. A. Griffiths, N. S. Hamilton, J. R. Hitchin, C. P. Hutton, S. Jones, P. Kelly, A. E. Mcgonagle, H. Small, A. I. Stowell, J. Tucker, I. D. Waddell, B. Waszkowycz, D. J. Ogilvie
First-In-Class Chemical Probes Against Poly(Adp-Ribose) Glycohydrolase (Parg) Inhibit Dna Repair With Differential Pharmacology To Olaparib.
Acs Chem. Biol. V. 11 3179 2016
PubMed-ID: 27689388  |  Reference-DOI: 10.1021/ACSCHEMBIO.6B00609

(-) Compounds

Molecule 1 - POLY(ADP-RIBOSE) GLYCOHYDROLASE
    ChainsA
    EC Number3.2.1.143
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid5116
    Expression System VariantGOLD
    GenePARG
    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  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
16WJ1Ligand/Ion1-(CYCLOPROPYLMETHYL)-6-[[(1-METHYLCYCLOPROPYL)AMINO]-BIS(OXIDANYL)-$L^{4}-SULFANYL]-3-[(2-METHYL-1,3-THIAZOL-5-YL)METHYL]QUINAZOLINE-2,4-DIONE
26WK1Mod. Amino Acid(2~{R})-2-AZANYL-3-[[(2~{S},3~{S})-2,3-BIS(OXIDANYL)-4-SULFANYL-BUTYL]DISULFANYL]PROPANOIC ACID
3DMS3Ligand/IonDIMETHYL SULFOXIDE
4SO43Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:725 , ILE A:726 , GLU A:727 , GLN A:754 , ARG A:758 , TYR A:792 , TYR A:795 , ASN A:869 , THR A:901 , PHE A:902binding site for residue 6WJ A 1001
2AC2SOFTWARECYS A:711 , GLU A:712 , THR A:924 , GLY A:926 , ASP A:927 , LYS A:930binding site for residue SO4 A 1002
3AC3SOFTWAREARG A:535 , TYR A:564 , ARG A:644 , ASN A:646 , ARG A:941binding site for residue SO4 A 1003
4AC4SOFTWAREPRO A:838 , ARG A:842 , HOH A:1258binding site for residue SO4 A 1004
5AC5SOFTWAREILE A:484 , ARG A:485 , VAL A:486 , PHE A:498binding site for residue DMS A 1005
6AC6SOFTWARETYR A:521 , LYS A:559 , TYR A:560 , ASN A:561 , VAL A:562 , HOH A:1265binding site for residue DMS A 1006
7AC7SOFTWAREPRO A:657 , ASP A:658 , GLY A:745 , ARG A:769binding site for residue DMS A 1007

(-) SS Bonds  (0, 0)

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

(-) 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 5LHB)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5LHB)

(-) 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:508
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhhh..................eee..hhhhh..............................eee.....eeehhhhhhhhhh....hhhhhhhhhhhhhhhhh....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeeeehhhhhhhhhhhhh.....................hhhhhh....hhhhhhhhhhhhhhhhhhh....eeeeeeee.....hhhhh......eeee...hhhhhh...eeeeee.............hhhhhhhhhhhhhhhhhhhh......eeeeee.....eeee.hhhhheeeee...............eeeeee.....hhhhhhhhhhhhhhhhhhhhhhh....hhhhh..eeee...hhhhh.hhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lhb A 450 DKKWLGTPIEEMRRMPRCGIRLPLLRPSANHTVTIRVDLLRAGEVPKPFPTHYKDLWDNKHVKMPCSEQNLYPVEERTAGSRWELIQTALLNKFTRPQNLKDAILKYNVAYSKKWDFTALIDFWDKVLEEAEAQHLYQSILPDMVKIALCLPNICTQPIPLLAAAMNHSITMSQEQIASLLANAFFCTFPRRNAKMKSEYSSYPDINFNRLFEGRSSRKPEKLKTLFxYFRRVTAAAPTGLVTFTRQSLEDFPEWERCEKPLTRLHVTYEGTIEENGQGMLQVDFANRFVGGGVTSAGLVQEEIRFLINPELIISRLFTEVLDHNECLIITGTEQYSEYTGYAETYRWSRSHEDGSERDDWQRRCTEIVAIDALHFRRYLDQFVPEKMRRELNKAYCGFLRPGVSSENLSAVATGNWGCGAFGGDARLKALIQILAAAAAERDVVYFTFGDSELMRDIYSMHIFLTERKLTVGDVYKLLLRYYNEECRNCSTPDIKLYPFIYHAVESC 963
                                   459       469       479       489       499       509       519    || 533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873       883       893       903       913       923       933       943 ||    955        
                                                                                                    524|                                                                                                                                                     681-6WK                                                                                                                                                                                                                                                                 945|               
                                                                                                     529                                                                                                                                                                                                                                                                                                                                                                                                                              948               

   Legend:   → Mismatch (orange background)
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  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 5LHB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Met A:464 - Pro A:465   [ RasMol ]  
    Phe A:498 - Pro A:499   [ RasMol ]  
 

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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 5a7r

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5LHB)