SMTL ID : 3qx3.1

Human topoisomerase IIbeta in complex with DNA and etoposide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.16 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, R.85, G.86, K.87, D.143, R.311, K.321, Q.324, Y.355, H.357, G.358, 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: EVP.3, MG.5 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Q.360 Hydrogen bonds: A:S.62, B:R.402 Water bridges: A:D.61, A:D.61, A:E.359, A:E.359, B:R.402 Salt bridges: A:K.38, B:R.402 DA-DG-DC-DC-DG-DA-DG-DC.2: 27 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, 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: EVP.8 29 PLIP interactions: 29 interactions with chain B Hydrophobic interactions: B:I.256, B:I.454 Hydrogen bonds: B:R.85, B:K.87, B:K.87, B:N.90, B:N.90, B:Q.98, B:R.402, B:G.457, B:A.459, B:T.592, B:T.594, B:N.596 Water bridges: B:N.102, B:N.102, B:A.250, B:A.250, B:F.251, B:R.259, B:K.260, B:R.311, B:K.461, B:K.461, B:T.594, B:T.594 Salt bridges: B:H.146, B:R.259, B:K.260

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.3: 10 residues within 4Å: Chain A: G.60, D.61, R.85, 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 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.85 Hydrogen bonds: A:D.61, A:D.61, A:D.61 Water bridges: A:R.85 EVP.8: 10 residues within 4Å: Chain B: G.60, D.61, R.85, 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 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:R.85 Hydrogen bonds: B:D.61, B:D.61, B:D.61 Water bridges: B:R.85

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

MG.4: 2 residues within 4Å: Chain A: D.139, D.141 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.139, A:D.141, H2O.11, H2O.12, H2O.35, H2O.35 MG.5: 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.6: 2 residues within 4Å: Chain B: D.139, D.141 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.139, B:D.141, H2O.18, H2O.25, H2O.27, H2O.38 MG.7: 2 residues within 4Å: Chain B: N.377, N.449 No protein-ligand interaction detected (PLIP) MG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, C.C. et al., Structural basis of type II topoisomerase inhibition by the anticancer drug etoposide. Science (2011)

Release Date

2011-07-06

Peptides

DNA topoisomerase 2-beta: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA topoisomerase 2-beta

Related Entries With Identical Sequence