4PJV: PARP2 catalytic domain

Structure of PARP2 catalytic domain bound to inhibitor BMN 673. Determined by X-ray diffraction at 2.5 Å resolution. Released 24 Sept 2014.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,331
Mol. weight: 84.69 kDa
Ligands: 2YQ
Released: 24 Sept 2014

Explore 4PJV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4PJV contains 34 α-helices and 36 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 16 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	236-245	10
α-helix	248-257	10
β-strand	260	1	1
α-helix	267-269	3
α-helix	272-291	20
α-helix	297-308	12
β-strand	311	1	1
α-helix	317-320	4
α-helix	324-346	23
α-helix	357-365	9
β-strand	367-371	5	2
α-helix	377-388	12
β-strand	398-409	12	2
α-helix	412-415	4
β-strand	423-429	7	2
α-helix	432-434	3
α-helix	435-441	7
α-helix	445-447	3
β-strand	461-463	3	3
β-strand	464	1	2
α-helix	467-472	6
β-strand	477	1	4
β-strand	480	1	4
β-strand	482-491	10	2
β-strand	495-498	4	3
β-strand	514-517	4	3
β-strand	519-523	5	5
α-helix	525-527	3
β-strand	529-531	3	2
β-strand	534-536	3	2
β-strand	541-543	3	5
β-strand	554-556	3	5
β-strand	558-561	4	3
α-helix	564-566	3
β-strand	567-578	12	2

Chain B: 18 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	236-245	10
α-helix	248-257	10
β-strand	260	1	6
α-helix	267-269	3
α-helix	272-288	17
α-helix	297-308	12
β-strand	311	1	6
α-helix	317-320	4
α-helix	324-346	23
α-helix	357-363	7
β-strand	367-371	5	7
α-helix	372-373	2
α-helix	377-388	12
β-strand	398-409	12	7
α-helix	412-415	4
β-strand	423-429	7	7
α-helix	432-434	3
α-helix	435-441	7
α-helix	445-447	3
α-helix	452-454	3
β-strand	461-463	3	8
β-strand	464	1	7
α-helix	467-471	5
β-strand	482-491	10	7
β-strand	495-498	4	8
β-strand	514-517	4	8
β-strand	519-523	5	9
α-helix	525-527	3
β-strand	529-531	3	7
β-strand	534-536	3	7
β-strand	541-543	3	9
β-strand	554-556	3	9
β-strand	558-561	4	8
α-helix	564-566	3
β-strand	567-578	12	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Poly [ADP-ribose] polymerase 2	A, B	protein	368	Homo sapiens	Q9UGN5 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4PJV_1 Poly [ADP-ribose] polymerase 2 (chains A, B)
MHHHHHHSSGVDLGTENLYFQSMDLRVQELIKLICNVQAMEEMMMEMKYNTKKAPLGKLT
VAQIKAGYQSLKKIEDCIRAGQHGRALMEACNEFYTRIPHDFGLRTPPLIRTQKELSEKI
QLLEALGDIEIAIKLVKTELQSPEHPLDQHYRNLHCALRPLDHESYEFKVISQYLQSTHA
PTHSDYTMTLLDLFEVEKDGEKEAFREDLHNRMLLWHGSRMSNWVGILSHGLRIAHPEAP
ITGYMFGKGIYFADMSSKSANYCFASRLKNTGLLLLSEVALGQCNELLEANPKAEGLLQG
KHSTKGLGKMAPSSAHFVTLNGSTVPLGPASDTGILNPDGYTLNYNEYIVYNPNQVRMRY
LLKVQFNF

Ligands and cofactors

ID	Name	Formula	Copies
2YQ	(8S,9R)-5-fluoro-8-(4-fluorophenyl)-9-(1-methyl-1H-1,2,4-triazol-5-yl)-2,7,8,9-…	C19 H14 F2 N6 O	2

Water and common crystallization additives (GOL) are not listed.

Primary citation

Structural basis for the inhibition of poly(ADP-ribose) polymerases 1 and 2 by BMN 673, a potent inhibitor derived from dihydropyridophthalazinone. Aoyagi-Scharber, M., Gardberg, A.S., Yip, B.K. et al. Acta Crystallogr F Struct Biol Commun (2014) 70:1143-1149. DOI 10.1107/S2053230X14015088 · PubMed

Other PDB entries of the same protein (UniProt Q9UGN5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4ZZX 1.65 Å, Structure of PARP2 catalytic domain bound to an isoindolinone inhibitor
5D5K 1.9 Å, Crystal Structure NLS from human PARP-2 complexed with Importin alpha delta IBB
3KJD 1.95 Å, Human poly(ADP-ribose) polymerase 2, catalytic fragment in complex with an inhibitor…
3KCZ 2.0 Å, Human poly(ADP-ribose) polymerase 2, catalytic fragment in complex with an inhibitor…
7R59 2.0 Å, PARP2 catalytic domain in complex with OUL245
4TVJ 2.1 Å, Human ARTD2 (PARP2) - catalytic domain in complex with olaparib
8HKO 2.1 Å, Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Rucaparib
9IM8 2.1 Å, Mutated ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to a pyrimidine…
9ZQB 2.1 Å, Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 1
4ZZY 2.2 Å, Structure of human PARP2 catalytic domain bound to an isoindolinone inhibitor
6F1K 2.2 Å, Structure of ARTD2/PARP2 WGR domain bound to double strand DNA without 5'phosphate
8HLJ 2.24 Å, Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Olaparib…

Browse structure collections

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