SMTL ID : 5gwi.1

Structure of a Human topoisomerase IIbeta fragment in complex with DNA and E7873R

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.74 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: 30 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, Q.360, A.361, T.365, N.368, K.396, 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: N2R.3, N2N.4, MG.6 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.400, B:Y.403, A:K.38, A:K.38 Hydrophobic interactions: A:Q.360 DA-DG-DC-DC-DG-DA-DG-DC.2: 31 residues within 4Å: Chain B: E.59, R.85, G.86, K.87, D.143, R.311, K.321, Q.324, Y.355, H.357, G.358, Q.360, A.361, T.365, N.368, K.396, 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: N2R.7, N2N.9, MG.11 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:R.85, B:K.87, B:K.87, B:N.90, B:N.90, B:N.90, B:Q.98, B:S.400, B:G.457, B:T.592, B:T.592, B:T.594, B:T.594, B:N.596 Salt bridges: B:H.146, B:R.259, B:K.260

4 x N2R: dichloro{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)

N2R.3: 14 residues within 4Å: Chain A: G.60, D.61, L.84, R.85, G.86, Q.360, M.363, M.364 Chain C: T.1, G.2 Chain D: A.4, G.5 Ligands: DA-DG-DC-DC-DG-DA-DG-DC.1, N2N.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 N2R.4: 15 residues within 4Å: Chain A: G.60, D.61, L.84, R.85, G.86, Q.360, M.363, M.364, P.401 Chain C: T.1, G.2 Chain D: A.4, G.5 Ligands: DA-DG-DC-DC-DG-DA-DG-DC.1, N2R.3 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.85 Hydrogen bonds: A:D.61, A:D.61, A:Q.360 N2R.7: 15 residues within 4Å: Chain B: G.60, D.61, L.84, R.85, G.86, Q.360, M.363, M.364 Chain C: C.3, A.4, G.5 Chain D: T.1, G.2 Ligands: DA-DG-DC-DC-DG-DA-DG-DC.2, N2N.9 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.61, B:D.61, B:D.61, B:Q.360 N2R.9: 16 residues within 4Å: Chain B: G.60, D.61, L.84, R.85, G.86, Q.360, M.363, M.364, P.401 Chain C: C.3, A.4, G.5 Chain D: T.1, G.2 Ligands: DA-DG-DC-DC-DG-DA-DG-DC.2, N2R.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.61, B:D.61, B:D.61, B:Q.360

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.1 MG.6: 4 residues within 4Å: Chain A: N.449, G.450, E.452 Ligands: DA-DG-DC-DC-DG-DA-DG-DC.1 No protein-ligand interaction detected (PLIP) MG.8: 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.4, H2O.7 MG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain B: N.449 Ligands: DA-DG-DC-DC-DG-DA-DG-DC.2 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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