SMTL ID : 4g0u.1

Human topoisomerase IIbeta in complex with DNA and amsacrine

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: 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, E.452, I.454, R.527, W.529 Chain C: T.1 Chain D: G.5, C.6, T.7, C.8, G.9, G.10, C.11, T.12 Ligands: ASW.9 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:D.61, A:D.61, A:S.62, A:S.62, A:R.85, B:R.402, B:R.402 Water bridges: A:A.63, A:G.358, A:Q.360, B:S.400 Salt bridges: B:R.402 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, Y.355, H.357, G.358, Q.360, 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 Chain D: T.1 Ligands: ASW.5 36 PLIP interactions: 36 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:R.402, B:R.402, B:G.457, B:T.592, B:T.594, B:T.594, B:T.594, B:N.596 Water bridges: B:K.87, B:Q.98, B:E.101, B:A.250, B:K.253, B:K.253, B:K.253, B:R.259, B:K.260, B:K.260, B:K.461, B:K.461, B:T.592, B:S.597, B:S.597, B:S.597, B:S.597 Salt bridges: B:H.146, B:R.259, B:K.260, B:K.461

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

MG.3: 3 residues within 4Å: Chain A: E.59, 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.1, H2O.4, H2O.6, H2O.14 MG.4: 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.7, H2O.11, H2O.13, H2O.16 MG.7: 3 residues within 4Å: Chain B: N.368, N.377, N.449 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain C: G.9, G.10 No protein-ligand interaction detected (PLIP) MG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x ASW: N-[4-(acridin-9-ylamino)-3-methoxyphenyl]methanesulfonamide(Non-covalent)

ASW.5: 12 residues within 4Å: Chain B: I.36, P.37, R.85, G.86, K.87, A.103, E.104, Q.360 Chain C: A.4, G.5 Chain D: T.1 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:R.85, B:E.104 Water bridges: B:E.104, B:E.104 ASW.9: 11 residues within 4Å: Chain A: P.37, R.85, G.86, K.87, A.103, E.104, Q.360 Chain C: T.1 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:R.85, A:E.104 Water bridges: A:E.104

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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