SMTL ID : 4j3n.1

Human Topoisomerase Iibeta in complex with DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 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: 26 residues within 4Å: Chain A: E.59, G.86, K.87, D.143, R.311, K.321, Q.324, Y.355, H.357, G.358, A.361, 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 11 PLIP interactions: 6 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:Q.360 Hydrogen bonds: A:K.38, A:D.61, A:E.359, B:S.400, B:R.402, B:R.402 Water bridges: A:S.62, A:S.62, B:S.400 Salt bridges: B:R.402 DA-DG-DC-DC-DG-DA-DG-DC.2: 26 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, A.361, 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 33 PLIP interactions: 33 interactions with chain B Hydrophobic interactions: B:I.256, B:I.454 Hydrogen bonds: B:R.85, B:R.85, B:K.87, B:K.87, B:N.90, B:N.90, B:Q.98, B:Q.360, B:G.457, B:A.459, B:T.592, B:T.594, B:N.596 Water bridges: B:G.86, B:K.87, B:N.102, B:A.250, B:A.250, B:F.251, B:R.259, B:R.311, B:K.461, B:K.461, B:L.593, B:T.594, B:T.594 Salt bridges: B:H.146, B:R.259, B:K.260 pi-Cation interactions: B:R.85, B:R.85

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

MG.3: 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.1, H2O.9, H2O.9, H2O.24 MG.4: 3 residues within 4Å: Chain A: N.449, G.450, E.452 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain A: F.304, D.308 Chain D: T.7, C.8 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.308, H2O.27 MG.6: 3 residues within 4Å: Chain B: E.59, 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.11, H2O.12, H2O.15, H2O.21 MG.7: 2 residues within 4Å: Chain B: N.377, N.449 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Chain C: G.10 No protein-ligand interaction detected (PLIP) MG.9: 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., On the structural basis and design guidelines for type II topoisomerase-targeting anticancer drugs. Nucleic Acids Res. (2013)

Release Date

2013-10-02

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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