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(-) Description

Title :  HUMAN ARTD1 (PARP1) - CATALYTIC DOMAIN IN COMPLEX WITH INHIBITOR NIRAPARIB
 
Authors :  T. Karlberg, A. G. Thorsell, J. Brock, H. Schuler
Date :  25 Aug 14  (Deposition) - 09 Sep 15  (Release) - 18 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Adp-Ribosylation, Dna Repair, Adp-Ribosyl Transferase, Transferase- Transferase Inhibitor Complex (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. 2016
PubMed-ID: 28001384

(-) Compounds

Molecule 1 - POLY [ADP-RIBOSE] POLYMERASE 1
    Chains: A, B, C, D
    EC Number: 2.4.2.30
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC-CH
    Expression System Strain: ROSETTA2(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN (UNP RESIDUES 662-1011)
    Gene: ADPRT, PARP1, PPOL
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PARP-1, ADP-RIBOSYLTRANSFERASE DIPHTHERIA TOXIN-LIKE 1, ARTD1, NAD(+) ADP-RIBOSYLTRANSFERASE 1, ADPRT 1, POLY[ADP-RIBOSE] SYNTHASE 1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
13JD4Ligand/Ion2-{4-[(3S)-PIPERIDIN-3-YL]PHENYL}-2H-INDAZOLE-7-CARBOXAMIDE
2GOL3Ligand/IonGLYCEROL
3SO44Ligand/IonSULFATE ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
13JD1Ligand/Ion2-{4-[(3S)-PIPERIDIN-3-YL]PHENYL}-2H-INDAZOLE-7-CARBOXAMIDE
2GOL1Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
13JD1Ligand/Ion2-{4-[(3S)-PIPERIDIN-3-YL]PHENYL}-2H-INDAZOLE-7-CARBOXAMIDE
2GOL1Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
Biological Unit 3 (3, 3)
No.NameCountTypeFull Name
13JD1Ligand/Ion2-{4-[(3S)-PIPERIDIN-3-YL]PHENYL}-2H-INDAZOLE-7-CARBOXAMIDE
2GOL1Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
13JD1Ligand/Ion2-{4-[(3S)-PIPERIDIN-3-YL]PHENYL}-2H-INDAZOLE-7-CARBOXAMIDE
2GOL-1Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:766 , HIS A:862 , GLY A:863 , GLY A:888 , TYR A:889 , TYR A:896 , PHE A:897 , SER A:904 , TYR A:907 , GOL A:1103BINDING SITE FOR RESIDUE 3JD A 1101
02AC2SOFTWARELYS A:903 , LEU A:984 , LEU A:985 , TYR A:986 , HOH A:1216BINDING SITE FOR RESIDUE SO4 A 1102
03AC3SOFTWAREHIS A:862 , TYR A:889 , ILE A:895 , TYR A:896 , 3JD A:1101 , HOH A:1206BINDING SITE FOR RESIDUE GOL A 1103
04AC4SOFTWAREGLU B:763 , ASP B:766 , HIS B:862 , GLY B:863 , GLY B:888 , TYR B:889 , TYR B:896 , PHE B:897 , SER B:904 , TYR B:907 , GOL B:1103BINDING SITE FOR RESIDUE 3JD B 1101
05AC5SOFTWARELYS B:903 , LEU B:984 , LEU B:985 , TYR B:986BINDING SITE FOR RESIDUE SO4 B 1102
06AC6SOFTWAREHIS B:862 , TYR B:889 , GLY B:894 , ILE B:895 , TYR B:896 , 3JD B:1101BINDING SITE FOR RESIDUE GOL B 1103
07AC7SOFTWAREASP C:766 , HIS C:862 , GLY C:863 , GLY C:888 , TYR C:889 , TYR C:896 , PHE C:897 , SER C:904 , TYR C:907 , GOL C:1103BINDING SITE FOR RESIDUE 3JD C 1101
08AC8SOFTWARELYS C:903 , LEU C:984 , LEU C:985 , TYR C:986 , HOH C:1232BINDING SITE FOR RESIDUE SO4 C 1102
09AC9SOFTWAREHIS C:862 , TYR C:889 , GLY C:894 , ILE C:895 , TYR C:896 , 3JD C:1101 , HOH C:1209 , HOH C:1243BINDING SITE FOR RESIDUE GOL C 1103
10BC1SOFTWAREASP D:766 , HIS D:862 , GLY D:863 , GLY D:888 , TYR D:889 , TYR D:896 , PHE D:897 , SER D:904 , TYR D:907BINDING SITE FOR RESIDUE 3JD D 1101
11BC2SOFTWARELYS D:903 , LEU D:984 , LEU D:985 , TYR D:986BINDING SITE FOR RESIDUE SO4 D 1102

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:845 -D:845
2B:845 -C:845

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4R6E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4R6E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R6E)

(-) Exons   (0, 0)

(no "Exon" information available for 4R6E)

(-) 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:350
                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.eeeee....hhhhhhhhhhhhhh.......eeeeeeeeeeeee.hhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhh..................eee..hhhhhhhhhh......eeeeeeeeee...eeee..............eeee.eeeee.hhhheee..eee....eee.......eee.eeee.hhh.eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4r6e A  661 MKSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKAEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFK 1010
                                   670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000      1010


Chain B from PDB  Type:PROTEIN  Length:350
                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.eeeee....hhhhhhhhhhhhhh.......eeeeeeeeeeeee.hhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhh..................eee..hhhhhhhhhh......eeeeeeeeee...eeee..............eeee.eeeee.hhhheee..eee....eee.......eee.eeee.hhh.eeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4r6e B  662 KSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKAEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKT 1011
                                   671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961       971       981       991      1001      1011


Chain C from PDB  Type:PROTEIN  Length:350
                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.eeeee....hhhhhhhhhhhhhh.......eeeeeeeeeeeee.hhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhh..................eee..hhhhhhhhhh......eeeeeeeeee...eeee..............eeee.eeeee.hhhheee..eee....eee.......eee.eeee.hhh.eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4r6e C  661 MKSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKAEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFK 1010
                                   670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000      1010


Chain D from PDB  Type:PROTEIN  Length:348
                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.eeeee....hhhhhhhhhhhhhh.......eeeeeeeeeeeee.hhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhh..................eee..hhhhhhhhhh......eeeeeeeeee...eeee..............eeee.eeeee.hhhheee..eee....eee.......eee.eeee.hhh.eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4r6e D  663 SKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKAEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFK 1010
                                   672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962       972       982       992      1002
   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 4R6E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R6E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R6E)

(-) Gene Ontology  (63, 63)

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  4r6e
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  PARP1_HUMAN | P09874
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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
        PARP1_HUMAN | P09874: 1uk0 1uk1 1wok 2cok 2cr9 2cs2 2dmj 2jvn 2l30 2l31 2n8a 2rcw 2rd6 2riq 3gjw 3gn7 3l3l 3l3m 3od8 3oda 3odc 3ode 4av1 4dqy 4gv7 4hhy 4hhz 4l6s 4opx 4oqa 4oqb 4pjt 4r5w 4rv6 4und 4uxb 4xhu 4zzz 5a00 5ds3 5ha9 5kpn 5kpo 5kpp 5kpq 5wrq 5wry 5wrz 5ws0 5ws1 5wtc

(-) Related Entries Specified in the PDB File

4r5w THE SAME PROTEIN COMPLEXED WITH XAV939
4und THE SAME PROTEIN COMPLEXED WITH BMN673
4uxb THE SAME PROTEIN COMPLEXED WITH PJ34