SMTL ID : 6cqi.1

2.42A Crystal structure of Mycobacterium tuberculosis Topoisomerase I in complex with an oligonucleotide MTS2-11

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.42 Å

Oligo State

monomer

Ligands

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1: 3 residues within 4Å: Chain A: D.53, L.54, R.56 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.56, A:D.60 FMT.2: 5 residues within 4Å: Chain A: H.50, R.52, D.53, Q.166, R.170 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.53, A:D.53, A:Q.166

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: R.578, F.584, W.605, F.609, S.620, V.621, A.622 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.578, A:R.578, A:V.621, A:A.622

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 4 residues within 4Å: Chain A: R.52, Y.85, W.123, E.127 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.127 Salt bridges: A:R.52 ACT.5: 3 residues within 4Å: Chain A: P.69, D.78, K.628 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.78 Salt bridges: A:K.628 ACT.6: 5 residues within 4Å: Chain A: S.319, R.323, F.324, K.554, S.557 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.554

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, N. et al., Investigating mycobacterial topoisomerase I mechanism from the analysis of metal and DNA substrate interactions at the active site. Nucleic Acids Res. (2018)

Release Date

2018-05-30

Peptides

DNA topoisomerase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA topoisomerase 1

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