SMTL ID : 5ino.1

Human Tdp2 reaction product (5'-phosphorylated DNA)-Mg2+ complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.21 Å

Oligo State

homo-dimer

Ligands

2 x DC- DC- DG- DA- DA- DT- DT- DC- DG: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')(Non-covalent)

DC-DC-DG-DA-DA-DT-DT-DC-DG.1: 25 residues within 4Å: Chain A: N.16, D.18, L.20, E.48, R.102, H.122, S.125, T.126, R.127, D.158, N.160, R.162, W.193, I.203, C.207, H.247 Chain B: I.203 Ligands: DC-DC-DG-DA-DA-DT-DT-DC-DG.2, DC-DC-DG-DA-DA-DT-DT-DC-DG.2, DC-DC-DG-DA-DA-DT-DT-DC-DG.2, DC-DC-DG-DA-DA-DT-DT-DC-DG.2, DC-DC-DG-DA-DA-DT-DT-DC-DG.2, DC-DC-DG-DA-DA-DT-DT-DC-DG.2, DC-DC-DG-DA-DA-DT-DT-DC-DG.2, DC-DC-DG-DA-DA-DT-DT-DC-DG.2 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DA-DA-DT-DT-DC-DG.2: 22 residues within 4Å: Chain A: G.202, I.203, T.204 Chain B: E.48, H.122, S.125, T.126, R.127, D.158, N.160, R.162, W.193, L.201, C.207 Ligands: DC-DC-DG-DA-DA-DT-DT-DC-DG.1, DC-DC-DG-DA-DA-DT-DT-DC-DG.1, DC-DC-DG-DA-DA-DT-DT-DC-DG.1, DC-DC-DG-DA-DA-DT-DT-DC-DG.1, DC-DC-DG-DA-DA-DT-DT-DC-DG.1, DC-DC-DG-DA-DA-DT-DT-DC-DG.1, DC-DC-DG-DA-DA-DT-DT-DC-DG.1, DC-DC-DG-DA-DA-DT-DT-DC-DG.1 Protein-ligand interaction information (PLIP) not available

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 2 residues within 4Å: Chain A: N.23, R.242 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.23 Salt bridges: A:R.242

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schellenberg, M.J. et al., Reversal of DNA damage induced Topoisomerase 2 DNA-protein crosslinks by Tdp2. Nucleic Acids Res. (2016)

Release Date

2016-04-27

Peptides

Tyrosyl-DNA phosphodiesterase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tyrosyl-DNA phosphodiesterase 2