SMTL ID : 8j9w.1

Cryo-EM structure of the African swine fever virus topoisomerase 2 complexed with Cut02bDNA and etoposide (EDI-2)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.539, D.541 Chain D: G.13 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.541 MG.2: 2 residues within 4Å: Chain B: D.539, D.541 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.541

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: 14 residues within 4Å: Chain A: G.439, D.440, G.471, G.472, M.756, S.757, T.760 Chain D: T.11, A.12, G.13 Chain E: G.4, C.5, T.6 Chain F: C.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.760 Hydrogen bonds: A:D.440, A:D.440 EVP.4: 13 residues within 4Å: Chain B: E.438, G.439, D.440, G.472, M.756, S.757 Chain C: T.11, A.12, G.13 Chain E: C.1 Chain F: G.4, C.5, T.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.440, B:D.440

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chang, C.M. et al., A unified view on enzyme catalysis by cryo-EM study of a DNA topoisomerase. Commun Chem (2024)

Release Date

2024-02-07

Peptides

DNA topoisomerase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA topoisomerase 2

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