SMTL ID : 6f1k.1

Structure of ARTD2/PARP2 WGR domain bound to double strand DNA without 5'phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 10 residues within 4Å: Chain A: M.29, Y.42, R.61, V.65, G.66, K.67, M.68 Chain E: L.35, N.40, V.65 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain A Hydrogen bonds: E:N.40, A:R.61, A:R.61, A:G.66 GOL.2: 10 residues within 4Å: Chain B: M.29, Y.42, R.61, V.65, G.66, K.67, M.68 Chain D: L.35, N.40, V.65 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:N.40, B:R.61, B:R.61, B:G.66 GOL.3: 10 residues within 4Å: Chain C: M.29, Y.42, R.61, V.65, G.66, K.67, M.68 Chain F: L.35, N.40, V.65 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:R.61, C:R.61, C:G.66, F:N.40 GOL.4: 10 residues within 4Å: Chain B: L.35, N.40, V.65 Chain D: M.29, Y.42, R.61, V.65, G.66, K.67, M.68 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:R.61, D:R.61, D:G.66, B:N.40 GOL.5: 10 residues within 4Å: Chain A: L.35, N.40, V.65 Chain E: M.29, Y.42, R.61, V.65, G.66, K.67, M.68 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:R.61, E:R.61, E:G.66, A:N.40 GOL.6: 10 residues within 4Å: Chain C: L.35, N.40, V.65 Chain F: M.29, Y.42, R.61, V.65, G.66, K.67, M.68 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain C Hydrogen bonds: F:R.61, F:R.61, F:G.66, C:N.40

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 3 residues within 4Å: Chain C: N.38 Chain G: G.18, G.19 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: N.38 Chain H: G.18, G.19 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: N.38 Chain I: G.18, G.19 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain F: N.38 Chain J: G.18, G.19 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain D: N.38 Chain K: G.18, G.19 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain E: N.38 Chain L: G.18, G.19 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Obaji, E. et al., Structural basis for DNA break recognition by ARTD2/PARP2. Nucleic Acids Res. (2018)

Release Date

2018-10-10

Peptides

Poly [ADP-ribose] polymerase 2: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Poly [ADP-ribose] polymerase 2