SMTL ID : 9bqa.1

Human Topoisomerase 2 Beta ATPase domain bound to BNS22 and non-hydrolyzable ATP analog AMPPNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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.4 20 PLIP interactions: 20 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:G.141, A:A.142, A:Q.351, A:Q.351, A:K.353 Water bridges: A:D.69, A:N.95, 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.8 20 PLIP interactions: 20 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:N.138, B:G.139, B:Y.140, B:G.141, B:A.142, B:Q.351, B:Q.351, B:K.353 Water bridges: B:E.62, B:N.95, B:T.190 Salt bridges: B:K.143

2 x 01: 8-(3,4-dihydroquinoline-1(2H)-carbonyl)-5,7-dimethoxy-4-propyl-2H-1-benzopyran-2-one

01.2: 22 residues within 4Å: Chain A: L.32, Q.34, F.35, M.36, W.37, F.52, P.54, Y.57, L.213, R.216, R.217, D.220, Y.245, Y.249, Q.285, I.286, S.287, F.288, A.293, T.294, T.295, E.354 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:M.36, A:F.52, A:I.286, A:F.288, A:T.295, A:T.295 Hydrogen bonds: A:Q.34, A:W.37 Salt bridges: A:R.216 01.6: 22 residues within 4Å: Chain B: L.32, Q.34, F.35, M.36, W.37, F.52, P.54, Y.57, L.213, R.216, R.217, D.220, Y.245, Y.249, Q.285, I.286, S.287, F.288, A.293, T.294, T.295, E.354 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:M.36, B:F.52, B:I.286, B:F.288, B:T.295, B:T.295 Hydrogen bonds: B:Q.34, B:W.37 Salt bridges: B:R.216

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 12 residues within 4Å: Chain A: S.224, R.226, F.242, L.267, N.269, E.270, R.271, W.272, D.273, N.340, C.341, L.342 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.226, A:R.271, A:D.273, A:D.273, A:D.273, A:N.340 Water bridges: A:S.224, A:R.226, A:F.242 GOL.7: 12 residues within 4Å: Chain B: S.224, R.226, F.242, L.267, N.269, E.270, R.271, W.272, D.273, N.340, C.341, L.342 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.226, B:R.271, B:D.273, B:D.273, B:N.340 Water bridges: B:S.224, B:R.226, B:F.242

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: N.66, G.136, G.141 Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain B: N.66, G.136, G.141 Ligands: ANP.5 No protein-ligand interaction detected (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-beta: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

DNA topoisomerase 2-beta

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