SMTL ID : 9bq9.1

Human Topoisomerase 2 Alpha ATPase domain bound to obex 5c and non-hydrolyzable ATP analog AMPPNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

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

ANP.1: 25 residues within 4Å: Chain A: E.62, N.66, N.70, R.73, N.95, 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 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:N.66, A:N.95, A:S.123, 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:K.143, A:T.190, A:Q.351, A:Q.351, A:K.353, A:K.353 Water bridges: A:N.66 Salt bridges: A:K.143 ANP.6: 25 residues within 4Å: Chain A: Y.9 Chain B: E.62, N.66, N.70, R.73, N.95, 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.7 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:N.66, B:N.95, B:S.123, B:S.124, B:S.124, B:N.125, B:R.137, B:N.138, B:G.139, B:Y.140, B:Y.140, B:G.141, B:A.142, B:K.143, B:Q.351, B:Q.351, B:K.353, B:K.353 Salt bridges: B:K.143

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: E.62, N.66 Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain B: N.66 Ligands: ANP.6 No protein-ligand interaction detected (PLIP)

2 x 01: 8-(3,4-dihydroquinoline-1(2H)-carbonyl)-7-(2-hydroxyethoxy)-4-propyl-2H-1-benzopyran-2-one

01.3: 19 residues within 4Å: Chain A: Q.35, M.36, W.37, Y.47, F.52, P.54, Y.57, R.216, D.220, Y.245, Y.249, Q.285, I.286, S.287, F.288, A.293, T.294, S.295, E.354 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.52, A:P.54, A:Y.57, A:I.286, A:F.288, A:A.293 Hydrogen bonds: A:W.37, A:W.37 Salt bridges: A:R.216 01.8: 16 residues within 4Å: Chain B: M.36, W.37, Y.47, Y.57, R.216, D.220, Y.245, Y.249, 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:Y.57, B:I.286, B:F.288, B:A.293 Hydrogen bonds: B:W.37 Water bridges: B:W.37, B:Q.284 Salt bridges: B:R.216

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: L.31, V.32, T.33 Chain B: Q.359, K.361 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:V.32, A:T.33, B:K.361 Water bridges: B:Q.359

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

CL.5: 5 residues within 4Å: Chain A: 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

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

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