SMTL ID : 7zbg.1

Human Topoisomerase II Beta ATPase ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 25 residues within 4Å: Chain A: N.63, A.64, N.67, R.70, N.92, K.95, I.97, I.113, F.114, T.119, S.120, S.121, N.122, G.133, R.134, N.135, G.136, Y.137, G.138, A.139, K.140, T.187 Chain B: Y.6 Ligands: SO4.2, MG.6 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:N.63, A:D.66, A:N.92, A:S.121, A:S.121, A:N.122, A:R.134, A:N.135, A:G.136, A:Y.137, A:A.139 Water bridges: A:N.92, A:G.138, A:G.138, A:T.187 Salt bridges: A:K.140 ADP.8: 25 residues within 4Å: Chain A: Y.6 Chain B: N.63, A.64, N.67, R.70, N.92, K.95, I.97, I.113, F.114, T.119, S.120, S.121, N.122, G.133, R.134, N.135, G.136, Y.137, G.138, A.139, K.140, T.187 Ligands: SO4.9, MG.13 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:N.63, B:N.92, B:S.121, B:S.121, B:S.121, B:N.122, B:R.134, B:N.135, B:G.136, B:Y.137, B:A.139, B:T.187 Water bridges: B:N.92, B:N.92, B:G.138, B:G.138 Salt bridges: B:K.140

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 12 residues within 4Å: Chain A: K.55, E.59, G.133, R.134, N.135, G.136, Y.137, G.138, K.350 Ligands: ADP.1, ITH.7, ITH.14 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.59, A:N.135, A:N.135, A:G.136, A:Y.137, A:G.138 Salt bridges: A:K.55, A:K.350 SO4.3: 6 residues within 4Å: Chain A: A.219, R.223, G.224, V.225, N.237, G.238 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.224, A:V.225, A:N.237, A:G.238 Salt bridges: A:R.223 SO4.4: 2 residues within 4Å: Chain A: D.204, K.205 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.205 SO4.5: 3 residues within 4Å: Chain A: K.159, H.160, H.180 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.160, A:H.180 SO4.9: 12 residues within 4Å: Chain B: K.55, E.59, G.133, R.134, N.135, G.136, Y.137, G.138, K.350 Ligands: ITH.7, ADP.8, ITH.14 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.59, B:N.135, B:N.135, B:G.136, B:Y.137, B:G.138 Salt bridges: B:K.55, B:K.350 SO4.10: 6 residues within 4Å: Chain B: A.219, R.223, G.224, V.225, N.237, G.238 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.224, B:V.225, B:N.237, B:G.238 Salt bridges: B:R.223 SO4.11: 2 residues within 4Å: Chain B: D.204, K.205 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.205 SO4.12: 3 residues within 4Å: Chain B: K.159, H.160, H.180 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.160, B:H.180

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 5 residues within 4Å: Chain A: E.59, N.63, G.133, G.138 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.13: 5 residues within 4Å: Chain B: E.59, N.63, G.133, G.138 Ligands: ADP.8 No protein-ligand interaction detected (PLIP)

2 x ITH: 4-[(2S,3R)-3-[3,5-bis(oxidanylidene)piperazin-1-ium-1-yl]butan-2-yl]piperazin-4-ium-2,6-dione(Non-covalent)

ITH.7: 18 residues within 4Å: Chain A: H.14, T.21, Y.22, N.135, Y.137, L.141, Q.348 Chain B: H.14, T.21, Y.22, K.55, N.135, Y.137, L.141, Q.348 Ligands: SO4.2, SO4.9, ITH.14 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.22, B:Q.348 Hydrogen bonds: B:T.21, B:K.55, B:N.135 pi-Cation interactions: A:Y.137 ITH.14: 18 residues within 4Å: Chain A: H.14, T.21, Y.22, K.55, N.135, Y.137, L.141, Q.348 Chain B: H.14, T.21, Y.22, N.135, Y.137, L.141, Q.348 Ligands: SO4.2, ITH.7, SO4.9 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.22, A:Q.348 Hydrogen bonds: A:K.55, A:N.135, B:T.21 pi-Cation interactions: B:Y.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ling, E.M. et al., A comprehensive structural analysis of the ATPase domain of human DNA topoisomerase II beta bound to AMPPNP, ADP, and the bisdioxopiperazine, ICRF193. Structure (2022)

Release Date

2022-05-25

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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