SMTL ID : 9caj.1

Human TOP3B-TDRD3 core complex in pre-cleavage state with ssDNA 5'-ACAGATATT-3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

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

DA-DC-DA-DG-DA-DT-DA-DT-DT.1: 34 residues within 4Å: Chain A: E.10, K.11, P.12, S.13, A.36, C.59, D.66, N.72, W.74, E.122, R.182, Q.183, D.186, L.187, G.190, C.191, T.194, R.195, L.212, S.214, G.216, P.217, C.218, Q.219, R.339, G.510, T.511, A.513, S.514, V.517, H.518, R.525, R.562 Ligands: MN.2 Protein-ligand interaction information (PLIP) not available

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

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

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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