SMTL ID : 7qfo.1

Human Topoisomerase II Beta ATPase AMPPNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x ALA: ALANINE(Non-covalent)

ALA.1: 5 residues within 4Å: Chain A: Q.327, S.382, I.383, L.384, N.385 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain A Hydrogen bonds: A.1, A:L.384 ALA.4: 5 residues within 4Å: Chain B: Q.327, S.382, I.383, L.384, N.385 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain B Hydrogen bonds: A.4, B:L.384

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

ANP.2: 27 residues within 4Å: Chain A: E.59, 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, Q.348, K.350 Chain B: Y.6 Ligands: MG.3 21 PLIP interactions: 20 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.63, A:N.92, A:S.120, A:S.121, A:S.121, A:S.121, A:N.122, A:R.134, A:N.135, A:G.136, A:Y.137, A:G.138, A:A.139, A:Q.348, A:Q.348, A:K.350 Water bridges: A:E.59, A:E.59, A:N.92, B:Y.6 Salt bridges: A:K.140 ANP.5: 27 residues within 4Å: Chain A: Y.6 Chain B: E.59, 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, Q.348, K.350 Ligands: MG.6 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:N.63, B:N.92, B:S.121, B:S.121, B:N.122, B:R.134, B:N.135, B:G.136, B:Y.137, B:G.138, B:A.139, B:T.187, B:Q.348, B:Q.348, B:K.350 Water bridges: B:E.59, B:N.63, B:D.66, B:N.92 Salt bridges: B:K.140

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: N.63, G.133, G.138 Ligands: ANP.2 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain B: N.63, G.133, G.138 Ligands: ANP.5 No protein-ligand interaction detected (PLIP)

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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