SMTL ID : 9cak.1

Human TOP3B-TDRD3 core complex in DNA rejoining state with ssDNA 5'-GACAGATATT-3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x DG- DA- DC- DA- DG- DA- DT: DNA (5'-D(P*GP*AP*CP*AP*GP*AP*T)-3')(Non-covalent)

DG-DA-DC-DA-DG-DA-DT.1: 35 residues within 4Å: Chain A: E.10, H.61, T.64, L.65, D.66, N.72, W.74, E.122, R.182, Q.183, D.186, L.187, G.190, C.191, T.194, R.195, T.198, Q.202, L.212, S.214, F.215, G.216, P.217, C.218, Q.219, Y.337, G.510, T.511, A.513, S.514, H.518, R.525, R.562 Ligands: DA-DT-DT.2, MN.3 Protein-ligand interaction information (PLIP) not available

1 x DA- DT- DT: DNA (5'-D(*AP*TP*T)-3')(Non-covalent)

DA-DT-DT.2: 11 residues within 4Å: Chain A: M.11, G.35, A.36, C.59, G.60, E.327, Y.330, T.331, Y.337, R.339 Ligands: DG-DA-DC-DA-DG-DA-DT.1 Protein-ligand interaction information (PLIP) not available

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 5 residues within 4Å: Chain A: E.10, D.118, D.120, Y.337 Ligands: DG-DA-DC-DA-DG-DA-DT.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.10, A:D.118, A:Y.337 MN.4: 2 residues within 4Å: Chain A: E.341, D.512 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.341, A:D.512

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, X. et al., Structural insights into human topoisomerase 3 beta DNA and RNA catalysis and nucleic acid gate dynamics. Nat Commun (2025)

Release Date

2025-02-05

Peptides

DNA topoisomerase 3-beta-1: A
Tudor domain-containing protein 3: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA topoisomerase 3-beta-1

Tudor domain-containing protein 3

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