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(-) Description

Title :  HUMAN ARTD1 (PARP1) CATALYTIC DOMAIN IN COMPLEX WITH INHIBITOR RUCAPARIB
 
Authors :  T. Karlberg, A. G. Thorsell, H. Schuler
Date :  25 Nov 14  (Deposition) - 09 Dec 15  (Release) - 09 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.19
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-Ribosyl Transferase, Adp-Ribosylation, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Karlberg, A. G. Thorsell, H. Schuler
Human Artd1 (Parp1) Catalytic Domain In Complex With Inhibitor Rucaparib.
To Be Published
PubMed: search

(-) 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-BSA4
    Expression System Strain: ROSETTA2(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC PARP 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  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1RPB2Ligand/IonRUCAPARIB
2SO46Ligand/IonSULFATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1RPB1Ligand/IonRUCAPARIB
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1RPB1Ligand/IonRUCAPARIB
2SO42Ligand/IonSULFATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1RPB-1Ligand/IonRUCAPARIB
2SO41Ligand/IonSULFATE ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1RPB-1Ligand/IonRUCAPARIB
2SO41Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:702 , LYS A:703 , ARG A:704 , GLU A:772 , LYS D:798 , GLN D:875BINDING SITE FOR RESIDUE SO4 A 1101
2AC2SOFTWARELYS A:903 , LEU A:984 , LEU A:985 , TYR A:986BINDING SITE FOR RESIDUE SO4 A 1102
3AC3SOFTWAREGLN A:759 , GLU A:763 , HIS A:862 , GLY A:863 , TYR A:896 , PHE A:897 , ALA A:898 , SER A:904 , TYR A:907 , GLU A:988BINDING SITE FOR RESIDUE RPB A 1103
4AC4SOFTWARESER B:702 , LYS B:703 , ARG B:704 , LYS C:798 , GLN C:875BINDING SITE FOR RESIDUE SO4 B 1101
5AC5SOFTWARELYS B:903 , LEU B:984 , LEU B:985 , TYR B:986BINDING SITE FOR RESIDUE SO4 B 1102
6AC6SOFTWAREGLU B:763 , HIS B:862 , GLY B:863 , THR B:887 , GLY B:888 , TYR B:896 , PHE B:897 , ALA B:898 , LYS B:903 , SER B:904 , TYR B:907BINDING SITE FOR RESIDUE RPB B 1103
7AC7SOFTWARELYS B:798 , GLN B:875 , SER C:702 , LYS C:703 , ARG C:704BINDING SITE FOR RESIDUE SO4 C 1101
8AC8SOFTWARELYS A:798 , GLN A:875 , SER D:702 , LYS D:703 , ARG D:704BINDING SITE FOR RESIDUE SO4 D 1101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4RV6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4RV6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4RV6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4RV6)

(-) Exons   (0, 0)

(no "Exon" information available for 4RV6)

(-) 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:347
                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh.eeeee....hhhhhhhhhhhhhh.......eeeeeeeeeeeee.hhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhh..................eeee.hhhhhhhh........eeeeeeeeee...eeee..............eeee.eeeee.hhhheee..eee....eee.......eee.eeee.hhh.eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4rv6 A  662 KSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKAEMLDNLLDIEVAYSLLRGGSDSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFK 1010
                                   671       681       691       701       711       721       731       741       751       761       771       781 ||    793       803       813       823       833       843       853       863       873       883       893       903       913       923       933       943       953       963       973       983       993      1003       
                                                                                                                                                   783|                                                                                                                                                                                                                                
                                                                                                                                                    786                                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:349
                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.eeeee....hhhhhhhhhhhhhh.......eeeeeeeeeeeee.hhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhh..................eeee.hhhhhhhh........eeeeeeeeee...eeee..............eeee.eeeee.hhhheee..eee....eee.......eee.eeee.hhh.eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4rv6 B  662 KSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKAEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFK 1010
                                   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         


Chain C from PDB  Type:PROTEIN  Length:347
                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh.eeeee....hhhhhhhhhhhhhh.......eeeeeeeeeeeee.hhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhh..................eeee.hhhhhhhh........eeeeeeeeee...eeee..............eeee.eeeee.hhhheee..eee....eee.......eee.eeee.hhh.eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4rv6 C  662 KSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKAEMLDNLLDIEVAYSLLRGGSSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFK 1010
                                   671       681       691       701       711       721       731       741       751       761       771       781||     793       803       813       823       833       843       853       863       873       883       893       903       913       923       933       943       953       963       973       983       993      1003       
                                                                                                                                                  782|                                                                                                                                                                                                                                 
                                                                                                                                                   785                                                                                                                                                                                                                                 


Chain D from PDB  Type:PROTEIN  Length:349
                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.eeeee....hhhhhhhhhhhhhh.......eeeeeeeeeeeee.hhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhh..................eeee.hhhhhhhh........eeeeeeeeee...eeee..............eeee.eeeee.hhhheee..eee....eee.......eee.eeee.hhh.eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4rv6 D  662 KSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKAEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFK 1010
                                   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
   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 4RV6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4RV6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4RV6)

(-) Gene Ontology  (63, 63)

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  4rv6
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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 4r6e 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
4r6e THE SAME PROTEIN COMPLEXED WITH NIRAPARIB
4und THE SAME PROTEIN COMPLEXED WITH BMN673
4uxb THE SAME PROTEIN COMPLEXED WITH PJ34