SMTL ID : 6pcm.1 (1 other biounit)

Crystal Structure of Mycobacterium smegmatis Topoisomerase I with ssDNA bound to both N- and C-terminal domains

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.11 Å

Oligo State

monomer

Ligands

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 2 residues within 4Å: Chain A: R.376, Q.377 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.377 Salt bridges: A:H.372, A:R.376 SO4.2: 2 residues within 4Å: Chain A: V.137, R.154 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.154 SO4.3: 3 residues within 4Å: Chain A: K.31, Y.35, D.397 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.397 Salt bridges: A:K.31 SO4.4: 3 residues within 4Å: Chain A: T.253, G.254, R.255 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.253, A:T.253, A:G.254, A:R.255 Salt bridges: A:R.255 SO4.5: 2 residues within 4Å: Chain A: T.824, E.825 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.825 SO4.6: 2 residues within 4Å: Chain A: R.210, P.511 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.210 SO4.7: 5 residues within 4Å: Chain A: R.321, F.322, S.323, E.517, K.550 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.550 SO4.8: 3 residues within 4Å: Chain A: R.656, R.659, E.665 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.656, A:R.659 SO4.9: 1 residues within 4Å: Chain A: Q.677 No protein-ligand interaction detected (PLIP) SO4.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.11: 3 residues within 4Å: Chain B: G.7, C.8, G.9 No protein-ligand interaction detected (PLIP) SO4.12: 4 residues within 4Å: Chain A: R.54 Chain B: C.15, C.16, G.17 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, N. et al., Mechanistic insights from structure of Mycobacterium smegmatis topoisomerase I with ssDNA bound to both N- and C-terminal domains. Nucleic Acids Res. (2020)

Release Date

2020-03-25

Peptides

DNA topoisomerase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA topoisomerase 1

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