SMTL ID : 5gwj.1

Structure of a Human topoisomerase IIbeta fragment in complex with DNA and E7873S

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.57 Å

Oligo State

homo-dimer

Ligands

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

DA-DG-DC-DC-DG-DA-DG-DC.1: 26 residues within 4Å: Chain A: E.59, G.86, K.87, D.143, R.311, K.321, Q.324, Y.355, H.357, G.358, T.365, N.368, E.452, I.454, R.527, W.529 Chain D: G.5, C.6, T.7, C.8, G.9, G.10, C.11, T.12 Ligands: N2S.3, N2W.4 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.402, B:R.402, A:Q.360 Salt bridges: B:R.402, A:K.38 DA-DG-DC-DC-DG-DA-DG-DC.2: 28 residues within 4Å: Chain B: E.59, G.86, K.87, D.143, R.311, K.321, Q.324, Y.355, H.357, G.358, A.361, T.365, N.368, E.452, I.454, R.527, W.529 Chain C: G.5, C.6, T.7, C.8, G.9, G.10, C.11, T.12 Ligands: N2S.7, N2W.8, MG.9 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:I.256, B:I.454 Hydrogen bonds: B:K.87, B:K.87, B:N.90, B:N.90, B:Q.98, B:N.102, B:R.402, B:R.402, B:G.457, B:T.592, B:T.594, B:N.596 Water bridges: B:R.311, B:A.459, B:A.459 Salt bridges: B:H.146, B:R.259, B:K.260

4 x N2S: chloro{4,5-di(amino-kappaN)-N-[9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydro-2H-furo[3',4':6,7]naphtho[2,3-d][1,3]dioxol-5-yl]pentanamide}platinum(Non-covalent)

N2S.3: 12 residues within 4Å: Chain A: G.60, D.61, R.85, G.86, Q.360, M.364 Chain C: T.1, G.2 Chain D: A.4, G.5 Ligands: DA-DG-DC-DC-DG-DA-DG-DC.1, N2W.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.85 Hydrogen bonds: A:D.61, A:D.61, A:Q.360 N2S.4: 12 residues within 4Å: Chain A: G.60, D.61, R.85, G.86, Q.360, M.364 Chain C: T.1, G.2 Chain D: A.4, G.5 Ligands: DA-DG-DC-DC-DG-DA-DG-DC.1, N2S.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.85, A:Q.360 Hydrogen bonds: A:D.61, A:D.61, A:Q.360 N2S.7: 13 residues within 4Å: Chain B: G.60, D.61, L.84, R.85, G.86, Q.360, M.364 Chain C: A.4, G.5 Chain D: T.1, G.2 Ligands: DA-DG-DC-DC-DG-DA-DG-DC.2, N2W.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.61 N2S.8: 13 residues within 4Å: Chain B: G.60, D.61, L.84, R.85, G.86, Q.360, M.364 Chain C: A.4, G.5 Chain D: T.1, G.2 Ligands: DA-DG-DC-DC-DG-DA-DG-DC.2, N2S.7 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.360 Hydrogen bonds: B:D.61

6 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.5: 2 residues within 4Å: Chain A: D.139, D.141 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.139, A:D.141, H2O.11 MG.6: 2 residues within 4Å: Chain A: N.449, G.450 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:N.449 MG.9: 3 residues within 4Å: Chain B: N.449, G.450 Ligands: DA-DG-DC-DC-DG-DA-DG-DC.2 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain B: D.139, D.141 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.139, B:D.141, H2O.9, H2O.10 MG.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y.R. et al., Producing irreversible topoisomerase II-mediated DNA breaks by site-specific Pt(II)-methionine coordination chemistry. Nucleic Acids Res. (2017)

Release Date

2017-08-23

Peptides

DNA topoisomerase 2-beta: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA topoisomerase 2-beta

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