SMTL ID : 9bqb.1

Human Topoisomerase 2 Alpha ATPase domain bound to topobexin and non-hydrolyzable ATP analog AMPPNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 27 residues within 4Å: Chain A: E.62, N.66, A.67, N.70, R.73, N.95, K.98, I.100, I.116, F.117, T.122, S.123, S.124, N.125, G.136, R.137, N.138, G.139, Y.140, G.141, A.142, K.143, T.190, Q.351, K.353 Chain B: Y.9 Ligands: MG.2 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:N.66, A:N.95, A:S.123, A:S.124, A:S.124, A:S.124, A:S.124, A:N.125, A:R.137, A:N.138, A:N.138, A:G.139, A:Y.140, A:Y.140, A:G.141, A:A.142, A:Q.351, A:Q.351, A:K.353 Water bridges: A:T.190 Salt bridges: A:K.143 ANP.5: 27 residues within 4Å: Chain A: Y.9 Chain B: E.62, N.66, A.67, N.70, R.73, N.95, K.98, I.100, I.116, F.117, T.122, S.123, S.124, N.125, G.136, R.137, N.138, G.139, Y.140, G.141, A.142, K.143, T.190, Q.351, K.353 Ligands: MG.6 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:N.66, B:N.95, B:S.123, B:S.124, B:S.124, B:S.124, B:S.124, B:N.125, B:R.137, B:N.138, B:N.138, B:G.139, B:Y.140, B:Y.140, B:G.141, B:A.142, B:Q.351, B:Q.351, B:K.353 Water bridges: B:N.95, B:T.190 Salt bridges: B:K.143

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: N.66, G.136, G.141 Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain B: N.66, G.136, G.141 Ligands: ANP.5 No protein-ligand interaction detected (PLIP)

2 x 01: 8-(3,4-dihydroquinoline-1(2H)-carbonyl)-7-[2-(4-methylpiperazin-1-yl)ethoxy]-4-propyl-2H-1-benzopyran-2-one

01.3: 23 residues within 4Å: Chain A: Q.34, Q.35, M.36, W.37, Y.47, F.52, P.54, Y.57, R.216, R.217, D.220, Y.245, Y.249, K.281, Q.284, Q.285, I.286, S.287, F.288, A.293, T.294, S.295, E.354 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.52, A:P.54, A:Y.57, A:F.288 Hydrogen bonds: A:W.37, A:Y.47 Water bridges: A:R.217 Salt bridges: A:R.216 01.8: 23 residues within 4Å: Chain B: Q.34, Q.35, M.36, W.37, Y.47, F.52, P.54, Y.57, R.216, R.217, D.220, Y.245, Y.249, K.281, Q.284, Q.285, I.286, S.287, F.288, A.293, T.294, S.295, E.354 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.52, B:P.54, B:Y.57, B:F.288 Hydrogen bonds: B:W.37, B:Y.47 Water bridges: B:R.217 Salt bridges: B:R.216

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 6 residues within 4Å: Chain A: F.348, D.349, S.350, K.353, E.354, N.355 Ligand excluded by PLIP CL.9: 6 residues within 4Å: Chain B: F.348, D.349, S.350, K.353, E.354, N.355 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 8 residues within 4Å: Chain B: Y.39, E.41, V.215, Y.219, L.232, N.235, L.237, P.238 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.219, B:N.235

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kubes, J. et al., Topobexin targets the Topoisomerase II ATPase domain for beta isoform-selective inhibition and anthracycline cardioprotection. Nat Commun (2025)

Release Date

2025-06-25

Peptides

DNA topoisomerase 2-alpha: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA topoisomerase 2-alpha

Related Entries With Identical Sequence