SMTL ID : 8df9.1

Structure of M. kandleri topoisomerase V in complex with DNA. 38 base pair asymmetric DNA complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.24 Å

Oligo State

homo-dimer

Ligands

12 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 3 residues within 4Å: Chain A: A.450, V.452, V.455 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:A.450 MG.2: 4 residues within 4Å: Chain A: T.414, K.415, K.416, V.419 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.414, A:K.416 MG.3: 3 residues within 4Å: Chain A: I.471, I.473, I.476 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:I.471, A:I.473, A:I.476 MG.4: 1 residues within 4Å: Chain A: D.384 No protein-ligand interaction detected (PLIP) MG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.6: 6 residues within 4Å: Chain B: I.471, I.473, R.474, G.475, I.476 Chain C: T.9 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:I.471, B:I.473, B:I.476 MG.7: 4 residues within 4Å: Chain B: A.450, V.452, V.455 Chain D: G.21 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:A.450 MG.8: 5 residues within 4Å: Chain B: T.414, K.415, K.416, V.419 Chain C: G.19 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.414, B:K.416 MG.9: 4 residues within 4Å: Chain B: L.735, V.737, I.740 Chain C: G.12 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:L.735, B:V.737, B:I.740 MG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x K: POTASSIUM ION(Non-functional Binders)

K.13: 4 residues within 4Å: Chain C: T.16, T.17 Chain D: T.19, T.20 No protein-ligand interaction detected (PLIP) K.14: 4 residues within 4Å: Chain C: T.23, C.24 Chain D: T.12, T.13 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Osterman, A. et al., Structures of topoisomerase V in complex with DNA reveal unusual DNA binding mode and novel relaxation mechanism. Elife (2022)

Release Date

2022-08-31

Peptides

Topoisomerase V: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Topoisomerase V

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