SMTL ID : 8czq.1

The crystal structure of MtbTOP1 in complex with both G- and T-segments

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.78 Å

Oligo State

monomer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: R.72, E.179, K.628, V.631, G.632 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.610, A:Y.610

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

ACT.2: 1 residues within 4Å: Chain A: R.32 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.32 ACT.3: 2 residues within 4Å: Chain A: Y.37, R.149 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.149 ACT.4: 7 residues within 4Å: Chain A: D.53, L.54, P.55, R.56, I.86, S.88, P.89 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.56 ACT.5: 4 residues within 4Å: Chain A: H.575, F.576, G.577, R.578 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.577, A:R.578

8 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PO4.7: 2 residues within 4Å: Ligands: PO4.8, PO4.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.302 PO4.8: 1 residues within 4Å: Ligands: PO4.7 No protein-ligand interaction detected (PLIP) PO4.9: 2 residues within 4Å: Ligands: PO4.10, PO4.13 No protein-ligand interaction detected (PLIP) PO4.10: 4 residues within 4Å: Chain C: C.12 Chain D: C.12 Ligands: PO4.9, PO4.13 No protein-ligand interaction detected (PLIP) PO4.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PO4.12: 1 residues within 4Å: Ligands: PO4.7 No protein-ligand interaction detected (PLIP) PO4.13: 2 residues within 4Å: Ligands: PO4.9, PO4.10 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ferdous, S. et al., The interaction between transport-segment DNA and topoisomerase IA-crystal structure of MtbTOP1 in complex with both G- and T-segments. Nucleic Acids Res. (2023)

Release Date

2022-12-14

Peptides

DNA topoisomerase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA topoisomerase 1

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