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(-) Description

Title :  STRUCTURE OF PARP2 CATALYTIC DOMAIN BOUND TO INHIBITOR BMN 673
 
Authors :  M. Aoyagi-Scharber, A. S. Gardberg, T. L. Edwards
Date :  12 May 14  (Deposition) - 24 Sep 14  (Release) - 24 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Parp2, Inhibitor, Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Aoyagi-Scharber, A. S. Gardberg, B. K. Yip, B. Wang, Y. Shen, P. A. Fitzpatrick
Structural Basis For The Inhibition Of Poly(Adp-Ribose) Polymerases 1 And 2 By Bmn 673, A Potent Inhibitor Derived From Dihydropyridophthalazinone.
Acta Crystallogr. , Sect. F V. 70 1143 2014
PubMed-ID: 25195882  |  Reference-DOI: 10.1107/S2053230X14015088

(-) Compounds

Molecule 1 - POLY [ADP-RIBOSE] POLYMERASE 2
    Chains: A, B
    EC Number: 2.4.2.30
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: NEB T7 EXPRESS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: PARP2 HELICAL AND CATALYTIC DOMAINS (UNP RESIDUES 235-579)
    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
12YQ2Ligand/Ion(8S,9R)-5-FLUORO-8-(4-FLUOROPHENYL)-9-(1-METHYL-1H-1,2,4-TRIAZOL-5-YL)-2,7,8,9-TETRAHYDRO-3H-PYRIDO[4,3,2-DE]PHTHALAZIN-3-ONE
2GOL3Ligand/IonGLYCEROL
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
12YQ1Ligand/Ion(8S,9R)-5-FLUORO-8-(4-FLUOROPHENYL)-9-(1-METHYL-1H-1,2,4-TRIAZOL-5-YL)-2,7,8,9-TETRAHYDRO-3H-PYRIDO[4,3,2-DE]PHTHALAZIN-3-ONE
2GOL2Ligand/IonGLYCEROL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
12YQ1Ligand/Ion(8S,9R)-5-FLUORO-8-(4-FLUOROPHENYL)-9-(1-METHYL-1H-1,2,4-TRIAZOL-5-YL)-2,7,8,9-TETRAHYDRO-3H-PYRIDO[4,3,2-DE]PHTHALAZIN-3-ONE
2GOL1Ligand/IonGLYCEROL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:328 , GLN A:332 , GLU A:335 , HIS A:428 , GLY A:429 , GLY A:454 , TYR A:455 , TYR A:462 , PHE A:463 , LYS A:469 , SER A:470 , TYR A:473 , GLU A:558 , GOL A:602 , HOH A:729 , HOH A:756 , HOH A:765binding site for residue 2YQ A 601
2AC2SOFTWAREGLU A:335 , ASP A:339 , HIS A:428 , SER A:430 , LEU A:443 , ARG A:444 , 2YQ A:601 , HOH A:765binding site for residue GOL A 602
3AC3SOFTWAREASP A:396 , TYR A:397 , ALA A:471 , ASN A:472 , PHE A:475 , ALA A:476binding site for residue GOL A 603
4AC4SOFTWARESER B:328 , GLN B:332 , GLU B:335 , HIS B:428 , GLY B:429 , GLY B:454 , TYR B:462 , PHE B:463 , ALA B:464 , LYS B:469 , SER B:470 , TYR B:473 , GLU B:558 , HOH B:723 , HOH B:726 , HOH B:741binding site for residue 2YQ B 601
5AC5SOFTWAREASP B:396 , ALA B:471 , ASN B:472 , PHE B:475 , ALA B:476binding site for residue GOL B 602

(-) SS Bonds  (0, 0)

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

(-) 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 4PJV)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PJV)

(-) 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:339
                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhheeeee....hhhhhhhhhhhhhh........eeeeeeeeeeee.hhhhhh......eeeeeee.hhhhhhhhhhhh..................eee..hhhhhhhh...hhhh.eeeeeeeeee...eeee...............eeee.eeeee.hhhheee..eee....eee..........eee.eeee.hhh.eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pjv A 234 MDLRVQELIKLICNVQAMEEMMMEMKYNTKKAPLGKLTVAQIKAGYQSLKKIEDCIRAGRALMEACNEFYTRIPHDFGLRTPPLIRTQKELSEKIQLLEALGDIEIAIKLVKTEEHPLDQHYRNLHCALRPLDHESYEFKVISQYLQSTHAPTHSDYTMTLLDLFEVEKDGEKEAFREDLHNRMLLWHGSRMSNWVGILSHGLRIAHPEAPITGYMFGKGIYFADMSSKSANYCFASRLKNTGLLLLSEVALGQCNELLEANPKAEGLLQGKHSTKGLGKMAPSSAHFVTLNGSTVPLGPASDTGILNPDGYTLNYNEYIVYNPNQVRMRYLLKVQFNF 579
                                   243       253       263       273       283       296       306       316       326       336       346   ||  360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570         
                                                                                    292|                                                   350|                                                                                                                                                                                                                                
                                                                                     296                                                    355                                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:330
                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh..eeeee....hhhhhhhhhhhhhh........eeeeeeeeeeee.hhhhhh......eeeeeee.hhhhhhhhhhhh........hhhhh.....eee..hhhhhhh.........eeeeeeeeee...eeee...............eeee.eeeee.hhhheee..eee....eee.......eee.eeee.hhh.eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4pjv B 234 MDLRVQELIKLICNVQAMEEMMMEMKYNTKKAPLGKLTVAQIKAGYQSLKKIEDCIRALMEACNEFYTRIPHDFGLRTPPLIRTQKELSEKIQLLEALGDIEIAIKLVKHPLDQHYRNLHCALRPLDHESYEFKVISQYLQSTHAPTHSDYTMTLLDLFEVEKDGEKEAFREDLHNRMLLWHGSRMSNWVGILSHGLRIAHPEAPITGYMFGKGIYFADMSSKSANYCFASRLKNTGLLLLSEVALGQCNELLEANPKAEGLLQGKHSTKGLGKMAPSSAHFVTLNGSTVPLGPASDTGILGYTLNYNEYIVYNPNQVRMRYLLKVQFNF 579
                                   243       253       263       273       283     ||299       309       319       329       339       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546||     559       569       579
                                                                                 289|                                                 348|                                                                                                                                                                                            547|                            
                                                                                  296                                                  356                                                                                                                                                                                             551
   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 4PJV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)

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        PARP2_HUMAN | Q9UGN5: 3kcz 3kjd 4tvj 4zzx 4zzy 5d5k 5dsy

(-) Related Entries Specified in the PDB File

4pjt