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(-) Description

Title :  HUMAN ARTD1 (PARP1) - CATALYTIC DOMAIN IN COMPLEX WITH INHIBITOR XAV939
 
Authors :  T. Karlberg, A. G. Thorsell, H. Schuler
Date :  22 Aug 14  (Deposition) - 02 Sep 15  (Release) - 18 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.84
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (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
    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

  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, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1SO47Ligand/IonSULFATE ION
2XAV2Ligand/Ion2-[4-(TRIFLUOROMETHYL)PHENYL]-7,8-DIHYDRO-5H-THIOPYRANO[4,3-D]PYRIMIDIN-4-OL
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
2XAV1Ligand/Ion2-[4-(TRIFLUOROMETHYL)PHENYL]-7,8-DIHYDRO-5H-THIOPYRANO[4,3-D]PYRIMIDIN-4-OL
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2XAV1Ligand/Ion2-[4-(TRIFLUOROMETHYL)PHENYL]-7,8-DIHYDRO-5H-THIOPYRANO[4,3-D]PYRIMIDIN-4-OL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:702 , LYS A:703 , ARG A:704 , GLU A:772 , LYS B:798 , GLN B:875BINDING SITE FOR RESIDUE SO4 A 1101
2AC2SOFTWARELYS A:903 , LEU A:985 , TYR A:986 , HIS B:1016BINDING SITE FOR RESIDUE SO4 A 1102
3AC3SOFTWARETHR A:1011 , HIS A:1013 , ARG B:865 , HIS B:909BINDING SITE FOR RESIDUE SO4 A 1103
4AC4SOFTWAREARG A:865 , HIS A:909 , HIS B:1013BINDING SITE FOR RESIDUE SO4 A 1104
5AC5SOFTWAREASP A:766 , ALA A:880 , TYR A:889 , GLY A:894BINDING SITE FOR RESIDUE SO4 A 1105
6AC6SOFTWAREASP A:766 , ASN A:767 , HIS A:862 , GLY A:863 , SER A:864 , ASN A:868 , TYR A:896 , PHE A:897 , LYS A:903 , SER A:904 , TYR A:907BINDING SITE FOR RESIDUE XAV A 1106
7AC7SOFTWARELYS A:798 , GLN A:875 , SER B:702 , LYS B:703 , ARG B:704 , GLU B:772BINDING SITE FOR RESIDUE SO4 B 1101
8AC8SOFTWARELYS B:903 , LEU B:985 , TYR B:986BINDING SITE FOR RESIDUE SO4 B 1102
9AC9SOFTWAREASP B:766 , ASN B:767 , HIS B:862 , GLY B:863 , SER B:864 , ASN B:868 , TYR B:896 , PHE B:897 , SER B:904 , TYR B:907BINDING SITE FOR RESIDUE XAV B 1103

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4R5W)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Val A:979 -Asn A:980
2Val B:979 -Asn B:980

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4R5W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R5W)

(-) Exons   (0, 0)

(no "Exon" information available for 4R5W)

(-) 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:351
                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh.eeeee....hhhhhhhhhhhhhh.......eeeeeeeeeeeee.hhhhhhhhhhh...eeeeeeeehhhhhhhhhhhh........hhhhh.....eee..hhhhhhh.........eeeeeeeeee...eeee..............eeee...eee.hhhh.hhhhh......eee...........eeee.hhh.eeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4r5w A  661 MKSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKAEMLDNLLDIEVAYSLLRGGSSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKTAH 1013
                                   670       680       690       700       710       720       730       740       750       760       770       780 ||    792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962       972       982       992      1002      1012 
                                                                                                                                                   782|                                                                                                                                                                                                                                    
                                                                                                                                                    785                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:355
                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh.eeeee....hhhhhhhhhhhhhh.......eeeeeeeeeeeee.hhhhhhhhhhh...eeeeeeeehhhhhhhhhhhh........hhhhh.....eee..hhhhhhh.........eeeeeeeeee...eeee..............eeee...eee.hhhh.hhhhh......eee...........eeee.hhh.eeeeeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4r5w B  661 MKSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKAEMLDNLLDIEVAYSLLRGGSSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKTAHHHHH 1017
                                   670       680       690       700       710       720       730       740       750       760       770       780 ||    792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962       972       982       992      1002      1012     
                                                                                                                                                   782|                                                                                                                                                                                                                                        
                                                                                                                                                    785
   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 4R5W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R5W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R5W)

(-) Gene Ontology  (63, 63)

Asymmetric Unit(hide GO term definitions)

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  4r5w
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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 4r6e 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

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