SMTL ID : 5gwk.1

Human topoisomerase IIalpha in complex with DNA and etoposide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.15 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: 28 residues within 4Å: Chain A: E.59, G.86, K.87, D.143, R.311, K.321, Q.324, Y.355, H.356, H.357, G.358, S.361, T.365, N.368, E.452, I.454, W.529 Chain D: G.5, C.6, T.7, C.8, G.9, G.10, C.11, T.12 Ligands: MG.3, MG.4, EVP.10 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.402 DA-DG-DC-DC-DG-DA-DG-DC.2: 25 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, S.361, T.365, N.368, E.452, I.454, W.529 Chain C: G.5, C.6, T.7, C.8, G.9, G.10, C.11, T.12 Ligands: EVP.8 18 PLIP interactions: 18 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:G.457, B:S.459, B:S.592, B:S.592, B:T.594, B:N.596, B:N.596 Salt bridges: B:H.146, B:K.253, B:K.253, B:R.259

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

MG.3: 4 residues within 4Å: Chain A: E.59, D.139, D.141 Ligands: DA-DG-DC-DC-DG-DA-DG-DC.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.139, A:D.141 MG.4: 5 residues within 4Å: Chain A: N.377, N.449, E.452, R.527 Ligands: DA-DG-DC-DC-DG-DA-DG-DC.1 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain B: E.59, D.139, D.141 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.139, B:D.141 MG.6: 4 residues within 4Å: Chain B: S.376, N.377, N.449, R.527 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain C: G.9 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain D: G.9, G.10 No protein-ligand interaction detected (PLIP)

2 x EVP: (5S,5aR,8aR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol -5-yl 4,6-O-[(1R)-ethylidene]-beta-D-glucopyranoside(Non-covalent)

EVP.8: 9 residues within 4Å: Chain B: G.60, D.61, R.85, M.364 Chain C: A.4, G.5 Chain D: T.1, G.2 Ligands: DA-DG-DC-DC-DG-DA-DG-DC.2 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.61, B:D.61, B:D.61 EVP.10: 11 residues within 4Å: Chain A: E.59, G.60, D.61, R.85, M.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 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.85 Hydrogen bonds: A:D.61, A:D.61, A:D.61

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-alpha: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA topoisomerase 2-alpha