SMTL ID : 5zrf.1

Crystal structure of human topoisomerase II beta in complex with 5-iodouridine-containing-DNA and etoposide in space group p21

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: 25 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, I.454, W.529 Chain D: G.5, C.6, U.7, C.8, G.9, G.10, C.11, U.12 Ligands: EVP.9 1 PLIP interactions: 1 interactions with chain B Salt bridges: 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, U.7, C.8, G.9, G.10, C.11, U.12 Ligands: EVP.7 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A 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:G.457, B:A.459, B:N.596, B:N.596, B:S.597, A:Y.403, B:S.62 Water bridges: B:R.85, B:R.85, B:N.102, B:H.146, B:A.250, B:A.250, B:F.251, B:R.259 Salt bridges: B:H.146, B:R.259, B:K.260

6 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.3, H2O.4, H2O.7, H2O.18 MG.4: 2 residues within 4Å: Chain A: N.449, G.450 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:N.449 MG.5: 4 residues within 4Å: Chain B: S.376, N.377, N.449, G.450 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:N.449, H2O.15, H2O.19 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.10, H2O.14, H2O.19, H2O.20 MG.8: 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)

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.7: 11 residues within 4Å: Chain B: G.60, D.61, L.84, R.85, Q.360, M.364 Chain C: A.4, G.5 Chain D: U.1, G.2 Ligands: DA-DG-DC-DC-DG-DA-DG-DC.2 6 PLIP interactions: 6 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, B:Q.360 EVP.9: 10 residues within 4Å: Chain A: G.60, D.61, L.84, R.85, M.364 Chain C: U.1, G.2 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:D.61, A:D.61, A:D.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, S.F. et al., Structural insights into the gating of DNA passage by the topoisomerase II DNA-gate. Nat Commun (2018)

Release Date

2018-08-08

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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