SMTL ID : 5tvp.1 (3 other biounits)

SUMO2 bound to Mouse Tdp2 catalytic domain with a 5'-phosphorylated DNA ternary complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 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: 29 residues within 4Å: Chain A: N.16, D.18, E.48, H.122, S.125, T.126, R.127, D.158, N.160, R.162, W.193, L.201, I.203, Y.207, F.211, D.244, H.245 Chain B: L.201, R.202, I.203, P.204 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: 30 residues within 4Å: Chain A: K.99, H.129, R.202, I.203, P.204 Chain B: N.16, D.18, E.48, H.122, S.125, T.126, R.127, D.158, N.160, R.162, W.193, L.201, I.203, Y.207, F.211, D.244, H.245 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

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 6 residues within 4Å: Chain A: L.161, R.162, D.163, H.209, R.210, R.213 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.163, A:R.210 Water bridges: A:H.209, A:R.213 Salt bridges: A:H.209, A:R.213 PO4.6: 7 residues within 4Å: Chain B: L.161, R.162, D.163, H.209, R.210, R.213 Ligands: PO4.8 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:L.161, B:D.163, B:R.210 Water bridges: B:H.209 Salt bridges: B:H.209, B:R.213 PO4.8: 5 residues within 4Å: Chain B: D.163, W.180, R.210, R.213 Ligands: PO4.6 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.163 Water bridges: B:K.185, B:K.185, B:R.210, B:R.213 Salt bridges: B:R.210, B:R.213

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 3 residues within 4Å: Chain A: L.233, E.234, K.235 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.233, A:K.235 EDO.5: 6 residues within 4Å: Chain A: C.35, Y.39, V.231, G.232, L.233, E.234 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.39, A:Y.39, A:G.232, A:L.233, A:E.234 Water bridges: A:E.234

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

CL.7: 1 residues within 4Å: Chain B: K.235 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schellenberg, M.J. et al., ZATT (ZNF451)-mediated resolution of topoisomerase 2 DNA-protein cross-links. Science (2017)

Release Date

2017-10-11

Peptides

Tyrosyl-DNA phosphodiesterase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

B
E

Tyrosyl-DNA phosphodiesterase 2

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