SMTL ID : 6zy8.1

Cryo-EM structure of the entire Human topoisomerase II alpha in State 2

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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

ANP.1: 20 residues within 4Å: Chain A: E.87, N.91, N.120, I.125, I.141, F.142, T.147, S.148, S.149, N.150, G.161, R.162, N.163, G.164, Y.165, G.166, A.167, K.168, T.215, K.378 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:E.87, A:N.91, A:N.120, A:N.120, A:S.148, A:S.148, A:S.149, A:N.150, A:G.161, A:R.162, A:N.163, A:G.164, A:G.164, A:Y.165, A:G.166, A:A.167, A:K.378, A:K.378 Salt bridges: A:K.168 ANP.2: 19 residues within 4Å: Chain B: E.87, N.91, N.120, I.141, F.142, T.147, S.148, S.149, N.150, G.161, R.162, N.163, G.164, Y.165, G.166, A.167, K.168, T.215, K.378 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:E.87, B:N.91, B:N.120, B:N.120, B:S.148, B:S.149, B:N.150, B:R.162, B:N.163, B:G.164, B:Y.165, B:G.166, B:K.378, B:K.378 Salt bridges: B:K.168

2 x EVP: (5S,5aR,8aR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol -5-yl 4,6-O-[(1R)-ethylidene]-beta-D-glucopyranoside(Non-covalent)

EVP.3: 9 residues within 4Å: Chain B: G.462, D.463, R.487, M.762 Chain C: C.1, G.2 Chain D: G.13 Chain E: G.4, C.5 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.487 Hydrogen bonds: B:D.463, B:R.487 EVP.4: 9 residues within 4Å: Chain A: G.462, D.463, R.487, M.762 Chain C: G.4, C.5 Chain E: C.1, G.2 Chain F: G.13 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.487 Hydrogen bonds: A:D.463, A:R.487

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vanden Broeck, A. et al., Structural basis for allosteric regulation of Human Topoisomerase II alpha. Nat Commun (2021)

Release Date

2021-05-26

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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