SMTL ID : 4g0v.1

Human topoisomerase iibeta in complex with DNA and mitoxantrone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 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, I.147, R.311, K.321, Q.324, Y.355, H.357, G.358, Q.360, 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: MIX.3 16 PLIP interactions: 12 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Q.360 Hydrogen bonds: A:R.85, B:S.400, B:S.400, B:R.402 Water bridges: A:D.61, A:S.62, A:R.85, A:R.85, A:G.358, A:G.358, A:E.359, A:E.359, A:E.359, B:S.400 Salt bridges: A:K.38 DA-DG-DC-DC-DG-DA-DG-DC.2: 27 residues within 4Å: Chain B: E.59, G.86, K.87, D.143, I.147, 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: MIX.8 30 PLIP interactions: 30 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:N.102, B:S.400, B:G.457, B:T.592, B:T.594, B:T.594, B:N.596 Water bridges: B:R.85, B:A.250, B:A.250, B:F.251, B:K.253, B:K.253, B:K.253, B:R.259, B:K.260, B:R.311, B:Q.360, B:Q.360, B:Q.360, B:K.461 Salt bridges: B:H.146, B:R.259, B:K.260

2 x MIX: 1,4-DIHYDROXY-5,8-BIS({2-[(2-HYDROXYETHYL)AMINO]ETHYL}AMINO)-9,10-ANTHRACENEDIONE(Non-covalent)

MIX.3: 14 residues within 4Å: Chain A: R.85, G.86, K.87, I.88, L.89, N.102, E.104, Q.360, M.364 Chain C: T.1 Chain D: A.4, G.5, C.6 Ligands: DA-DG-DC-DC-DG-DA-DG-DC.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.85, A:L.89, A:N.102, A:N.102, A:E.104, A:Q.360, A:Q.360, A:Q.360 Water bridges: A:G.86, A:Q.360 MIX.8: 12 residues within 4Å: Chain B: R.85, G.86, K.87, N.102, E.104, Q.360, M.364 Chain C: A.4, G.5, C.6 Chain D: T.1 Ligands: DA-DG-DC-DC-DG-DA-DG-DC.2 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.85, B:N.102, B:E.104, B:Q.360, B:Q.360 Water bridges: B:G.86, B:Q.360

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.5, H2O.5, H2O.5, H2O.5 MG.5: 2 residues within 4Å: Chain A: N.377, N.449 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.13, H2O.13, H2O.15, H2O.21 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: 1 residues within 4Å: Chain A: K.253 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, C.C. et al., On the structural basis and design guidelines for type II topoisomerase-targeting anticancer drugs. Nucleic Acids Res. (2013)

Release Date

2013-07-17

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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