SMTL ID : 4g0w.1

Human topoisomerase iibeta in complex with DNA and ametantrone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 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: 27 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, 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: AKE.9 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.85, A:R.85, A:Q.360, B:S.400, B:S.400 Water bridges: A:D.61, A:S.62, A:G.358, B:S.400 Salt bridges: 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, I.147, 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 C: G.5, C.6, T.7, C.8, G.9, G.10, C.11, T.12 Ligands: MG.6, AKE.7, MG.8 31 PLIP interactions: 31 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:S.400, B:G.457, B:T.592, B:T.594, B:N.596 Water bridges: B:R.85, B:E.101, B:A.250, B:K.253, B:K.253, B:K.253, B:R.259, B:K.260, B:R.311, B:Q.360, B:E.452, B:A.459, B:T.594, B:S.597, B:S.597 Salt bridges: B:H.146, B:R.259, B:K.260

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

MG.3: 3 residues within 4Å: Chain A: E.59, D.139, D.141 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.139, A:D.141, H2O.4, H2O.4, H2O.13 MG.4: 2 residues within 4Å: Chain A: N.449, G.450 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:N.449, H2O.5, H2O.5, H2O.6, H2O.13 MG.5: 3 residues within 4Å: Chain B: E.59, D.139, D.141 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.139, B:D.141, H2O.11, H2O.11, H2O.11 MG.6: 4 residues within 4Å: Chain B: N.449, G.450, R.527 Ligands: DA-DG-DC-DC-DG-DA-DG-DC.2 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain C: G.9, G.10 Ligands: DA-DG-DC-DC-DG-DA-DG-DC.2, DA-DG-DC-DC-DG-DA-DG-DC.2 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Chain D: G.9 No protein-ligand interaction detected (PLIP)

2 x AKE: 1,4-bis({2-[(2-hydroxyethyl)amino]ethyl}amino)anthracene-9,10-dione(Non-covalent)

AKE.7: 14 residues within 4Å: Chain B: R.85, G.86, K.87, I.88, L.89, 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 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.85, B:L.89, B:N.102, B:Q.360 AKE.9: 13 residues within 4Å: Chain A: R.85, G.86, K.87, I.88, L.89, N.102, E.104, Q.360 Chain C: T.1 Chain D: A.4, G.5, C.6 Ligands: DA-DG-DC-DC-DG-DA-DG-DC.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.85, A:L.89, A:N.102, A:Q.360 Water bridges: A:R.85, A:Q.360

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

Related Entries With Identical Sequence