4PJT - JenaLib

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Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   STRUCTURE OF PARP1 CATALYTIC DOMAIN BOUND TO INHIBITOR BMN 673

Authors :   M. Aoyagi-Scharber, A. S. Gardberg, T. L. Arakaki

Date :   12 May 14 (Deposition) - 24 Sep 14 (Release) - 25 Feb 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.35

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 :   Parp1, Inhibitor, Complex, Transferase-Transferase 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

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	:	PET28A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	PARP1 HELICAL AND CATALYTIC DOMAINS (UNP RESIDUES 662- 1011)
	Gene	:	PARP1, ADPRT, 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

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
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)

Asymmetric Unit (3, 22)

No.	Name	Count	Type	Full Name
1	2YQ	4	Ligand/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
2	GOL	3	Ligand/Ion	GLYCEROL
3	SO4	15	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 7)

No.	Name	Count	Type	Full Name
1	2YQ	1	Ligand/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
2	GOL	2	Ligand/Ion	GLYCEROL
3	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	2YQ	1	Ligand/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
2	GOL	-1	Ligand/Ion	GLYCEROL
3	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 3 (3, 5)

No.	Name	Count	Type	Full Name
1	2YQ	1	Ligand/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
2	GOL	1	Ligand/Ion	GLYCEROL
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 4 (2, 4)

No.	Name	Count	Type	Full Name
1	2YQ	1	Ligand/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
2	GOL	-1	Ligand/Ion	GLYCEROL
3	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (22, 22)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS A:903 , LEU A:984 , LEU A:985 , TYR A:986	binding site for residue SO4 A 1101
02	AC2	SOFTWARE	ARG A:858 , MET A:929 , LYS A:949	binding site for residue SO4 A 1102
03	AC3	SOFTWARE	ARG A:841 , GLY A:843 , CYS A:845 , GLN A:846 , GLY B:843 , GLU B:844 , CYS B:845 , GLN B:846	binding site for residue SO4 A 1103
04	AC4	SOFTWARE	SER A:808 , GLU A:809 , GLU A:810 , HOH A:1286 , HIS C:937	binding site for residue SO4 A 1104
05	AC5	SOFTWARE	GLN A:759 , GLU A:763 , HIS A:862 , GLY A:863 , GLY A:888 , TYR A:889 , TYR A:896 , PHE A:897 , ALA A:898 , LYS A:903 , SER A:904 , TYR A:907 , GLU A:988 , HOH A:1220 , HOH A:1231 , HOH A:1272	binding site for residue 2YQ A 1105
06	AC6	SOFTWARE	LYS A:933 , HIS A:934 , ALA A:935 , SER A:936	binding site for residue GOL A 1106
07	AC7	SOFTWARE	GLY A:944 , HIS A:946 , PRO D:850 , LEU D:854 , HIS D:946	binding site for residue GOL A 1107
08	AC8	SOFTWARE	LYS B:903 , LEU B:984 , LEU B:985 , TYR B:986	binding site for residue SO4 B 1101
09	AC9	SOFTWARE	GLN A:846 , LYS A:849 , LYS B:838 , ASP B:965 , LYS B:1000 , HOH B:1241	binding site for residue SO4 B 1102
10	AD1	SOFTWARE	ARG B:858 , MET B:929 , LYS B:949	binding site for residue SO4 B 1103
11	AD2	SOFTWARE	LYS B:943 , GLY B:944 , HIS B:946 , SO4 B:1106 , HOH B:1234 , HIS C:946	binding site for residue SO4 B 1104
12	AD3	SOFTWARE	HIS B:862 , GLY B:863 , GLY B:888 , TYR B:889 , TYR B:896 , PHE B:897 , ALA B:898 , LYS B:903 , SER B:904 , TYR B:907 , GLU B:988 , HOH B:1221 , HOH B:1224	binding site for residue 2YQ B 1105
13	AD4	SOFTWARE	LYS B:945 , HIS B:946 , GLN B:996 , SO4 B:1104 , HOH B:1213	binding site for residue SO4 B 1106
14	AD5	SOFTWARE	LYS C:903 , LEU C:985 , TYR C:986 , GOL C:1105 , HOH C:1266	binding site for residue SO4 C 1101
15	AD6	SOFTWARE	LYS C:838 , LYS C:1000 , GLN D:846 , LYS D:849	binding site for residue SO4 C 1102
16	AD7	SOFTWARE	SER C:702 , LYS C:703 , ARG C:704	binding site for residue SO4 C 1103
17	AD8	SOFTWARE	GLN C:759 , HIS C:862 , GLY C:863 , GLY C:888 , TYR C:889 , TYR C:896 , PHE C:897 , ALA C:898 , LYS C:903 , SER C:904 , TYR C:907 , GLU C:988 , GOL C:1105 , HOH C:1224 , HOH C:1256	binding site for residue 2YQ C 1104
18	AD9	SOFTWARE	GLY C:888 , TYR C:889 , MET C:890 , TYR C:896 , GLU C:988 , SO4 C:1101 , 2YQ C:1104 , HOH C:1215	binding site for residue GOL C 1105
19	AE1	SOFTWARE	GLY C:843 , CYS C:845 , GLN C:846 , GLU D:842 , GLY D:843 , GLU D:844 , CYS D:845 , GLN D:846	binding site for residue SO4 D 1101
20	AE2	SOFTWARE	LYS D:903 , LEU D:984 , LEU D:985 , TYR D:986 , HOH D:1231	binding site for residue SO4 D 1102
21	AE3	SOFTWARE	ARG D:858 , MET D:929 , LYS D:949	binding site for residue SO4 D 1103
22	AE4	SOFTWARE	GLN D:759 , GLU D:763 , HIS D:862 , GLY D:863 , GLY D:888 , TYR D:889 , TYR D:896 , PHE D:897 , ALA D:898 , LYS D:903 , SER D:904 , TYR D:907 , GLU D:988 , HOH D:1212 , HOH D:1237 , HOH D:1242	binding site for residue 2YQ D 1104

Asymmetric Unit

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

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

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

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

(no "Exon" information available for 4PJT)

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:338
                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.eeeee....hhhhhhhhhhhhhh.......eeeeeeeeeeeee.hhhhhhhhhh....eeeeeee.hhhhhhhhhhhh..................eee..hhhhhhhhhh......eeeeeeeeee...eeee..............eeee.eeeee.hhhheee..eee....eee.......eee.eeee.hhh.eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4pjt A  662 KSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQDSQILDLSNRFYTLIPHDFKPPLLNNADSVQAKVEMLDNLLDIEVAYSLLRGSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFK 1010
                                   671       681       691       701       711       721||     734       744|      757       767       777  ||   792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962       972       982       992      1002        
                                                                                      722|               744|                             780|                                                                                                                                                                                                                                
                                                                                       726                748                              786

Chain B from PDB  Type:PROTEIN  Length:332
                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.eeeee....hhhhhhhhhhhhhh.......eeeeeeeeeeeee.hhhhhhhhhhh...eeeeeee.hhhhhhhhhhhh..................eee..hhhhhhhhhh......eeeeeeeeee...eeee............eeee.eeeee.hhhheee..eee....eee.......eee.eeee.hhh.eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4pjt B  662 KSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSDSQILDLSNRFYTLIPHDPLLNNADSVQAKVEMLDNLLDIEVAYSLLRGSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASSKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFK 1010
                                   671       681       691       701       711       721|      735       751       761       771       786       796       806       816       826       836       846       856       866       876       886       896       906       916       926       936|      948       958       968       978       988       998      1008  
                                                                                     721|              743|                           780|                                                                                                                                                   936|                                                                       
                                                                                      726               750                            786                                                                                                                                                    939

Chain C from PDB  Type:PROTEIN  Length:346
                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.eeeee....hhhhhhhhhhhhhh.......eeeeeeeeeeeee.hhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhh..................eee..hhhhhhhhhh......eeeeeeeeee...eeee...ee.........eeee.eeeee.hhhheee..eee....eee.......eee.eeee.hhh.eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4pjt C  662 KSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKVEMLDNLLDIEVAYSLLRGGSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFK 1010
                                   671       681       691       701       711       721       731       741       751       761       771       781|      794       804       814       824       834       844       854       864       874       884       894       904       914       924       934       944       954       964       974       984       994      1004      
                                                                                                                                                 781|                                                                                                                                                                                                                                 
                                                                                                                                                  785

Chain D from PDB  Type:PROTEIN  Length:326
                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.eeeee....hhhhhhhhhhhhhh........eeeeeeeeeeee.hhhhhhhhhh....eeeeeee.hhhhhhhhhhhh..................eee..hhhhhhhhhh......eeeeeeeeee...eeee..............eeee.eeeee.hhhheee..eee....eee.......eee.eeee.hhh.eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4pjt D  663 SKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSLDLSNRFYTLIPHDPPLLNNADSVQAKVEMLDNLLDIEVAYSLLRDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNF 1009
                                   672       682       692       702       712       730       740  ||   755       765       775   ||  793       803       813       823       833       843       853       863       873       883       893       903       913       923       933       943       953       963       973       983       993      1003      
                                                                                    721|          743|                           779|                                                                                                                                                                                                                             
                                                                                     730           749                            788

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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 '\|'

(no "SCOP Domain" information available for 4PJT)

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

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

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Description

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Ligands, Modified Residues, Ions (3, 22)

Sites (22, 22)

SS Bonds (2, 2)

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