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(-) Description

Title :  HUMAN ARTD2 (PARP2) - CATALYTIC DOMAIN IN COMPLEX WITH OLAPARIB
 
Authors :  T. Karlberg, A. G. Thorsell, T. Ekblad, A. F. Pinto, H. Schuler
Date :  27 Jun 14  (Deposition) - 08 Jul 15  (Release) - 22 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Poly(Adp-Ribose) Transferase, Inhibitor, Adp-Ribosylation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. G. Thorsell, T. Ekblad, T. Karlberg, M. Low, A. F. Pinto, L. Tresaugues, M. Moche, M. S. Cohen, H. Schuler
Structural Basis For Potency And Promiscuity In Poly(Adp-Ribose) Polymerase (Parp) And Tankyrase Inhibitors
J. Med. Chem. V. 60 1262 2017
PubMed-ID: 28001384  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B00990

(-) Compounds

Molecule 1 - POLY [ADP-RIBOSE] POLYMERASE 2
    Chains: A, B
    EC Number: 2.4.2.30
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PNIC28-BSA4
    Expression System Strain: R3 PRARE
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PARP2, ADPRT2, ADPRTL2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HPARP-2,ADP-RIBOSYLTRANSFERASE DIPHTHERIA TOXIN-LIKE 2, ARTD2,NAD(+) ADP-RIBOSYLTRANSFERASE 2,ADPRT-2,POLY[ADP-RIBOSE] SYNTHASE 2,PADPRT-2

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
109L2Ligand/Ion4-(3-{[4-(CYCLOPROPYLCARBONYL)PIPERAZIN-1-YL]CARBONYL}-4-FLUOROBENZYL)PHTHALAZIN-1(2H)-ONE
2GOL3Ligand/IonGLYCEROL
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
109L1Ligand/Ion4-(3-{[4-(CYCLOPROPYLCARBONYL)PIPERAZIN-1-YL]CARBONYL}-4-FLUOROBENZYL)PHTHALAZIN-1(2H)-ONE
2GOL2Ligand/IonGLYCEROL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
109L1Ligand/Ion4-(3-{[4-(CYCLOPROPYLCARBONYL)PIPERAZIN-1-YL]CARBONYL}-4-FLUOROBENZYL)PHTHALAZIN-1(2H)-ONE
2GOL1Ligand/IonGLYCEROL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:335 , HIS A:428 , GLY A:429 , ARG A:444 , TYR A:455 , GLY A:460 , ILE A:461 , TYR A:462 , PHE A:463 , SER A:470 , TYR A:473 , GOL A:603 , HOH A:723binding site for residue 09L A 601
2AC2SOFTWAREASP A:396 , TYR A:397 , ALA A:471 , ASN A:472 , PHE A:475 , ALA A:476binding site for residue GOL A 602
3AC3SOFTWARESER A:328 , ILE A:331 , GLU A:335 , GLY A:454 , TYR A:455 , 09L A:601 , HOH A:854binding site for residue GOL A 603
4AC4SOFTWAREGLU B:335 , HIS B:428 , GLY B:429 , ARG B:444 , TYR B:455 , GLY B:460 , ILE B:461 , TYR B:462 , SER B:470 , TYR B:473 , HOH B:719binding site for residue 09L B 601
5AC5SOFTWAREASP B:396 , TYR B:397 , ALA B:471 , ASN B:472 , CYS B:474 , PHE B:475 , ALA B:476binding site for residue GOL B 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4TVJ)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:539 -Pro A:540
2Gly B:539 -Pro B:540

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4TVJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4TVJ)

(-) Exons   (0, 0)

(no "Exon" information available for 4TVJ)

(-) 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:357
                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhheeeee....hhhhhhhhhhhhhh........eeeeeeeeeeee.hhhhhh......eeeeeee.hhhhhhhhhhhh........hhhhh.....eee..hhhhhhhhhh......eeeeeeeeee...eeee.....hhhhhh....eeee.eeeee.hhhheee..eee....eee..........eee.eeee.hhh.eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tvj A 223 DLGTENLYFQSMDLRVQELIKLICNVQAMEEMMMEMKYNTKKAPLGKLTVAQIKAGYQSLKKIEDCIRAGQHGRALMEACNEFYTRIPHDFGLRTPPLIRTQKELSEKIQLLEALGDIEIAIKLVKTELQSPEHPLDQHYRNLHCALRPLDHESYEFKVISQYLQSTHAPTHSDYTMTLLDLFEVEKDGEKEAFREDLHNRMLLWHGSRMSNWVGILSHGLRIAHPEAPITGYMFGKGIYFADMSSKSANYCFASRLKNTGLLLLSEVALGQCNELLEANPKAEGLLQGKHSTKGLGKMAPSSAHFVTLNGSTVPLGPASDTGILNPDGYTLNYNEYIVYNPNQVRMRYLLKVQFNF 579
                                   232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       


Chain B from PDB  Type:PROTEIN  Length:351
                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhheeeee....hhhhhhhhhhhhhh........eeeeeeeeeeee.hhhhhh......eeeeeee.hhhhhhhhhhhh........hhhhh.....eee..hhhhhhhh........eeeeeeeeee...eeee.....hhhhhh....eeee.eeeee.hhhheee..eee....eee..........eee.eeee.hhh.eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tvj B 226 TENLYFQSMDLRVQELIKLICNVQAMEEMMMEMKYNTKKAPLGKLTVAQIKAGYQSLKKIEDCIRAGQHGRALMEACNEFYTRIPHDFGLRTPPLIRTQKELSEKIQLLEALGDIEIAIKLVKTSPEHPLDQHYRNLHCALRPLDHESYEFKVISQYLQSTHAPTHSDYTMTLLDLFEVEKDGEKEAFREDLHNRMLLWHGSRMSNWVGILSHGLRIAHPEAPITGYMFGKGIYFADMSSKSANYCFASRLKNTGLLLLSEVALGQCNELLEANPKAEGLLQGKHSTKGLGKMAPSSAHFVTLNGSTVPLGPASDTGILNPDGYTLNYNEYIVYNPNQVRMRYLLKVQFNF 579
                                   235       245       255       265       275       285       295       305       315       325       335       345   ||  358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578 
                                                                                                                                                     349|                                                                                                                                                                                                                                  
                                                                                                                                                      353
   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 4TVJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4TVJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4TVJ)

(-) Gene Ontology  (16, 16)

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  PARP2_HUMAN | Q9UGN5
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  2.4.2.30
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 Related Entries

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

UniProtKB/Swiss-Prot
        PARP2_HUMAN | Q9UGN5: 3kcz 3kjd 4pjv 4zzx 4zzy 5d5k 5dsy

(-) Related Entries Specified in the PDB File

3kcz 3KCZ CONTAINS THE SAME PROTEIN COMPLEXED WITH 3-AMINOBENZAMIDE.
3kjd 3KJD CONTAINS THE SAME PROTEIN COMPLEXED WITH ABT-888 (VELIPARIB).