SMTL ID : 8ke7.1

Crystal structure of DNA binding and cleavage core of human topoisomerase 2-beta in a DNA binding-competent conformation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

9 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 5 residues within 4Å: Chain A: N.372, P.384, G.386, F.388, G.389 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.384 Hydrogen bonds: A:N.372, A:F.388, A:G.389 ACT.2: 6 residues within 4Å: Chain A: L.635, E.749, L.753, K.756, L.761, E.764 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.756 ACT.3: 5 residues within 4Å: Chain A: V.419, W.634, L.635, M.638, E.642 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.419, A:L.635 Water bridges: A:K.746, A:K.746 Salt bridges: A:K.746 ACT.4: 5 residues within 4Å: Chain A: K.326, L.427, Y.428, D.429, E.435 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.429 Salt bridges: A:K.326 ACT.5: 5 residues within 4Å: Chain A: H.146, A.250, F.251, F.304, S.305 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.250 Salt bridges: A:H.146 ACT.6: 5 residues within 4Å: Chain B: G.70, L.71, G.72, I.74, G.75 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.70, B:I.74, B:G.75 ACT.7: 4 residues within 4Å: Chain B: F.512, V.514, E.520, T.522 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.520 ACT.8: 4 residues within 4Å: Chain B: K.326, L.427, Y.428, E.435 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.326 ACT.9: 7 residues within 4Å: Chain B: V.419, W.634, L.635, M.638, L.639, E.642, K.746 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.635 Salt bridges: B:K.746

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, K.T. et al., Structural insights into the assembly of type IIA topoisomerase DNA cleavage-religation center. Nucleic Acids Res. (2024)

Release Date

2024-07-24

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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