SMTL ID : 4puq.1

Mus Musculus Tdp2 reaction product complex with 5'-phosphorylated RNA/DNA, glycerol, and Mg2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x C- DC- DG- DA- DA- DT- DT- DC- DG: DNA/RNA hybrid(Non-covalent)

C-DC-DG-DA-DA-DT-DT-DC-DG.1: 30 residues within 4Å: Chain A: P.204, A.205 Chain B: N.16, E.48, H.122, S.125, T.126, R.127, D.158, N.160, R.162, W.193, L.201, I.203, Y.207, H.209, F.211, D.244, H.245 Ligands: C-DC-DG-DA-DA-DT-DT-DC-DG.2, C-DC-DG-DA-DA-DT-DT-DC-DG.2, C-DC-DG-DA-DA-DT-DT-DC-DG.2, C-DC-DG-DA-DA-DT-DT-DC-DG.2, C-DC-DG-DA-DA-DT-DT-DC-DG.2, C-DC-DG-DA-DA-DT-DT-DC-DG.2, C-DC-DG-DA-DA-DT-DT-DC-DG.2, C-DC-DG-DA-DA-DT-DT-DC-DG.2, MG.4, GOL.5, GOL.8 Protein-ligand interaction information (PLIP) not available C-DC-DG-DA-DA-DT-DT-DC-DG.2: 29 residues within 4Å: Chain A: N.16, E.48, H.122, S.125, T.126, R.127, D.158, N.160, R.162, W.193, L.201, I.203, Y.207, H.209, F.211, H.245 Chain B: I.203, P.204 Ligands: C-DC-DG-DA-DA-DT-DT-DC-DG.1, C-DC-DG-DA-DA-DT-DT-DC-DG.1, C-DC-DG-DA-DA-DT-DT-DC-DG.1, C-DC-DG-DA-DA-DT-DT-DC-DG.1, C-DC-DG-DA-DA-DT-DT-DC-DG.1, C-DC-DG-DA-DA-DT-DT-DC-DG.1, C-DC-DG-DA-DA-DT-DT-DC-DG.1, C-DC-DG-DA-DA-DT-DT-DC-DG.1, MG.3, ACT.7, GOL.8 Protein-ligand interaction information (PLIP) not available

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: N.16, E.48 Ligands: C-DC-DG-DA-DA-DT-DT-DC-DG.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.48, H2O.5, H2O.8, H2O.8, H2O.24 MG.4: 4 residues within 4Å: Chain B: N.16, E.48 Ligands: C-DC-DG-DA-DA-DT-DT-DC-DG.1, GOL.5 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.48, H2O.16, H2O.17, H2O.17

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain B: L.20, E.48, Y.74, R.102, S.125 Ligands: C-DC-DG-DA-DA-DT-DT-DC-DG.1, MG.4 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.48, B:R.102, B:S.125, B:S.125 GOL.6: 6 residues within 4Å: Chain B: P.186, H.188, C.189, S.227, L.228, D.229 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.228, B:D.229 GOL.8: 5 residues within 4Å: Chain A: E.128 Ligands: C-DC-DG-DA-DA-DT-DT-DC-DG.1, C-DC-DG-DA-DA-DT-DT-DC-DG.2, C-DC-DG-DA-DA-DT-DT-DC-DG.2, C-DC-DG-DA-DA-DT-DT-DC-DG.2 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.128, A:E.128

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 4 residues within 4Å: Chain A: L.201, I.203 Ligands: C-DC-DG-DA-DA-DT-DT-DC-DG.2, C-DC-DG-DA-DA-DT-DT-DC-DG.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, R. et al., Proteolytic Degradation of Topoisomerase II (Top2) Enables the Processing of Top2DNA and Top2RNA Covalent Complexes by Tyrosyl-DNA-Phosphodiesterase 2 (TDP2). J.Biol.Chem. (2014)

Release Date

2014-05-14

Peptides

Tyrosyl-DNA phosphodiesterase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tyrosyl-DNA phosphodiesterase 2

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