3KJD: Poly [ADP-ribose] polymerase 2

Human poly(ADP-ribose) polymerase 2, catalytic fragment in complex with an inhibitor ABT-888. Determined by X-ray diffraction at 1.95 Å resolution. Released 17 Nov 2009.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,105
Mol. weight: 84.33 kDa
Ligands: 78P
Released: 17 Nov 2009

Explore 3KJD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3KJD contains 42 α-helices and 34 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: 21 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	227-231	5
α-helix	233-235	3
α-helix	236-245	10
α-helix	248-257	10
β-strand	260	1	1
α-helix	267-269	3
α-helix	272-290	19
α-helix	296-308	13
β-strand	311	1	1
α-helix	317-320	4
α-helix	324-347	24
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
α-helix	452-454	3
β-strand	461-463	3	3
β-strand	464	1	2
α-helix	467-472	6
β-strand	482-491	10	2
β-strand	495-498	4	3
α-helix	505-508	4
β-strand	514-517	4	3
α-helix	518	1
β-strand	519-523	5	4
α-helix	525-527	3
β-strand	529-531	3	2
β-strand	534-536	3	2
β-strand	541-543	3	4
β-strand	554-556	3	4
β-strand	558-561	4	3
α-helix	564-566	3
β-strand	567-578	12	2

Chain B: 21 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	224-231	8
α-helix	236-245	10
α-helix	248-257	10
β-strand	260	1	5
α-helix	267-269	3
α-helix	272-290	19
α-helix	296-308	13
β-strand	311	1	5
α-helix	317-320	4
α-helix	324-346	23
α-helix	357-365	9
β-strand	367-371	5	6
α-helix	372-373	2
α-helix	377-388	12
β-strand	398-409	12	6
α-helix	412-415	4
β-strand	423-429	7	6
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	7
β-strand	464	1	6
α-helix	467-472	6
β-strand	482-491	10	6
β-strand	495-498	4	7
α-helix	505-508	4
β-strand	514-517	4	7
α-helix	518	1
β-strand	519-523	5	8
α-helix	525-527	3
β-strand	529-531	3	6
β-strand	534-536	3	6
β-strand	541-543	3	8
β-strand	554-556	3	8
β-strand	558-561	4	7
α-helix	564-566	3
β-strand	567-578	12	6

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

>3KJD_1 Poly [ADP-ribose] polymerase 2 (chains A, B)
MHHHHHHSSGVDLGTENLYFQSMDLRVQELIKLICNVQAMEEMMMEMKYNTKKAPLGKLT
VAQIKAGYQSLKKIEDCIRAGQHGRALMEACNEFYTRIPHDFGLRTPPLIRTQKELSEKI
QLLEALGDIEIAIKLVKTELQSPEHPLDQHYRNLHCALRPLDHESYEFKVISQYLQSTHA
PTHSDYTMTLLDLFEVEKDGEKEAFREDLHNRMLLWHGSRMSNWVGILSHGLRIAHPEAP
ITGYMFGKGIYFADMSSKSANYCFASRLKNTGLLLLSEVALGQCNELLEANPKAEGLLQG
KHSTKGLGKMAPSSAHFVTLNGSTVPLGPASDTGILNPDGYTLNYNEYIVYNPNQVRMRY
LLKVQFNF

Ligands and cofactors

ID	Name	Formula	Copies
78P	(2R)-2-(7-carbamoyl-1H-benzimidazol-2-yl)-2-methylpyrrolidinium	C13 H16 N4 O	2

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

Primary citation

Crystal structure of the catalytic domain of human PARP2 in complex with PARP inhibitor ABT-888. Karlberg, T., Hammarstrom, M., Schutz, P. et al. Biochemistry (2010) 49:1056-1058. DOI 10.1021/bi902079y · 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
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…
9ZQC 2.37 Å, Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 2

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