6F5B: ARTD2/PARP2 WGR domain

Structure of ARTD2/PARP2 WGR domain bound to double stranded DNA with 5'phosphate. Determined by X-ray diffraction at 2.8 Å resolution. Released 10 Oct 2018.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 6
Atoms: 2,673
Mol. weight: 42.73 kDa
Released: 10 Oct 2018

Explore 6F5B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6F5B contains 4 α-helices and 16 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: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	93-95	3
β-strand	105-107	3	1
β-strand	109-110	2	2
β-strand	113-114	2	2
β-strand	116-123	8	1
β-strand	128-139	12	1
β-strand	145-153	9	1
β-strand	159-166	8	1
α-helix	169-184	16
β-strand	202	1	1

Chain B: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	93-95	3
β-strand	105-107	3	3
β-strand	109-110	2	4
β-strand	113-114	2	4
β-strand	116-123	8	3
β-strand	128-139	12	3
β-strand	145-153	9	3
β-strand	159-164	6	3
α-helix	169-184	16
β-strand	202	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Poly [ADP-ribose] polymerase 2	A, B	protein	131	Homo sapiens	Q9UGN5 (AlphaFold model)
DNA (5'-d(pgpcpcptpaptpapgpgpc)-3')	C, D, E, F	DNA	10	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>6F5B_1 Poly [ADP-ribose] polymerase 2 (chains A, B)
SMGKAPVDPECTAKVGKAHVYCEGNDVYDVMLNQTNLQFNNNKYYLIQLLEDDAQRNFSV
WMRWGRVGKMGQHSLVACSGNLNKAKEIFQKKFLDKTKNNWEDREKFEKVPGKYDMLQMD
YATNTQDEEET

Sequence of entity 2 (C, D, E, F), FASTA

>6F5B_2 DNA (5'-D(P*GP*CP*CP*TP*AP*TP*AP*GP*GP*C)-3') (chains C, D, E, F)
GCCTATAGGC

Primary citation

Structural basis for DNA break recognition by ARTD2/PARP2. Obaji, E., Haikarainen, T., Lehtio, L. Nucleic Acids Res (2018) 46:12154-12165. DOI 10.1093/nar/gky927 · 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…

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