8HKS: Poly [ADP-ribose] polymerase 2

Name: PDB 8HKS: Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Pamiparib(BGB-290)
Published: 2024-05-01
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Pamiparib(BGB-290). Determined by X-ray diffraction at 2.8 Å resolution. Released 1 May 2024.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 4
Atoms: 11,510
Mol. weight: 162.16 kDa
Ligands: DS9
Released: 1 May 2024

Explore 8HKS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8HKS contains 79 α-helices and 72 β-strands across 4 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: 20 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	230-232	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	397-409	13	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	467-471	5
α-helix	472-474	3
β-strand	482-491	10	2
β-strand	495-498	4	3
α-helix	505-508	4
β-strand	514-517	4	3
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	567-579	13	2

Chain B: 20 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	230-232	3
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	324-347	24
α-helix	357-364	8
β-strand	367-371	5	6
α-helix	377-388	12
β-strand	397-409	13	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	467-471	5
α-helix	472-474	3
β-strand	482-491	10	6
β-strand	495-498	4	7
α-helix	505-508	4
β-strand	510	1	8
β-strand	512	1	8
β-strand	514-517	4	7
β-strand	519-523	5	9
α-helix	525-527	3
β-strand	529-531	3	6
β-strand	534-536	3	6
β-strand	541-543	3	9
β-strand	554-556	3	9
β-strand	558-561	4	7
α-helix	564-566	3
β-strand	567-579	13	6

Chain C: 20 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	236-245	10
α-helix	248-257	10
β-strand	260	1	10
α-helix	267-269	3
α-helix	272-291	20
α-helix	296-308	13
β-strand	311	1	10
α-helix	317-320	4
α-helix	324-347	24
α-helix	350-351	2
α-helix	357-365	9
β-strand	367-371	5	11
α-helix	377-388	12
β-strand	397-409	13	11
α-helix	412-415	4
β-strand	423-430	8	11
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	12
β-strand	464	1	11
α-helix	467-471	5
α-helix	472-474	3
β-strand	482-491	10	11
β-strand	495-498	4	12
α-helix	505-508	4
β-strand	514-517	4	12
β-strand	519-523	5	13
α-helix	525-527	3
β-strand	529-531	3	11
β-strand	534-536	3	11
β-strand	541-543	3	13
β-strand	554-556	3	13
β-strand	558-561	4	12
α-helix	564-566	3
β-strand	567-579	13	11

Chain D: 19 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	231	1	14
α-helix	236-245	10
α-helix	248-257	10
β-strand	260	1	15
α-helix	267-269	3
α-helix	272-290	19
α-helix	296-308	13
β-strand	311	1	15
α-helix	317-321	5
α-helix	324-348	25
β-strand	355	1	14
α-helix	357-364	8
β-strand	367-371	5	16
α-helix	377-388	12
β-strand	397-409	13	16
α-helix	412-415	4
β-strand	423-429	7	16
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	17
β-strand	464	1	16
α-helix	467-472	6
β-strand	482-491	10	16
β-strand	495-498	4	17
α-helix	505-508	4
β-strand	514-517	4	17
β-strand	519-523	5	18
α-helix	525-527	3
β-strand	529-530	2	16
β-strand	535-536	2	16
β-strand	541-543	3	18
α-helix	544-546	3
β-strand	554-556	3	18
β-strand	558-561	4	17
α-helix	564-566	3
β-strand	567-579	13	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Poly [ADP-ribose] polymerase 2	A, B, C, D	protein	353	Homo sapiens	Q9UGN5 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>8HKS_1 Poly [ADP-ribose] polymerase 2 (chains A, B, C, D)
GPESQLDLRVQELIKLICNVQAMEEMMMEMKYNTKKAPLGKLTVAQIKAGYQSLKKIEDC
IRAGQHGRALMEACNEFYTRIPHDFGLRTPPLIRTQKELSEKIQLLEALGDIEIAIKLVK
SERQGLEHPLDQHYRNLHCALRPLDHESYEFKVISQYLQSTHAPTHSDYTMTLLDLFEVE
KDGEKEAFREDLHNRMLLWHGSRMSNWVGILSHGLRIAPPEAPITGYMFGKGIYFADMSS
KSANYCFASRLKNTGLLLLSEVALGQCNELLEANPKAEGLLQGKHSTKGLGKMAPSSAHF
VTLNGSTVPLGPASDTGILNPDGYTLNYNEYIVYNPNQVRMRYLLKVQFNFLQ

Ligands and cofactors

ID	Name	Formula	Copies
DS9	(2R)-14-fluoro-2-methyl-6,9,10,19-tetrazapentacyclo[14.2.1.02,6.08,18.012,17]no…	C16 H15 F N4 O	4

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

Primary citation

Engaging an engineered PARP-2 catalytic domain mutant to solve the complex structures harboring approved drugs for structure analyses. Wang, X., Zhou, J., Xu, B. Bioorg Chem (2025) 160:108471-108471. DOI 10.1016/j.bioorg.2025.108471 · 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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