SMTL ID : 7yq8.1

Cryo-EM structure of human topoisomerase II beta in complex with DNA and etoposide

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: D.562, D.564 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.562, A:D.564, A:D.564 MG.2: 2 residues within 4Å: Chain B: D.562, D.564 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.562, B:D.564, B:D.564

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.3: 13 residues within 4Å: Chain B: E.482, G.483, D.484, R.508, Q.783, M.787, P.824 Chain D: A.27, A.28 Chain E: G.22, T.23 Chain F: T.24, C.25 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.824 Hydrogen bonds: B:D.484 EVP.4: 11 residues within 4Å: Chain A: E.482, G.483, D.484, R.508, Q.783, M.787 Chain C: G.23 Chain D: C.24, A.25 Chain F: G.27, C.28 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.508 Hydrogen bonds: A:D.484

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bunch, H. et al., ERK2-topoisomerase II regulatory axis is important for gene activation in immediate early genes. Nat Commun (2023)

Release Date

2024-01-03

Peptides

DNA topoisomerase 2-beta: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA topoisomerase 2-beta