SMTL ID : 6waa.2 (1 other biounit)

K. pneumoniae Topoisomerase IV (ParE-ParC) in complex with DNA and compound 34 (7-[(1S,5R)-1-amino-3-azabicyclo[3.1.0]hexan-3-yl]-4-(aminomethyl)-1-cyclopropyl-3,6-difluoro-8-methylquinolin-2(1H)-one)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-dimer

Ligands

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 10 residues within 4Å: Chain A: R.617, L.621, L.624, A.661, E.664, L.665, K.666, H.669, E.674, I.678 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.624, A:L.665 Hydrogen bonds: A:R.617, A:R.617 MPD.5: 8 residues within 4Å: Chain B: K.358, S.359, F.360, A.361, A.362 Chain E: A.2, T.3, C.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.358, B:F.360 MPD.6: 9 residues within 4Å: Chain B: R.617, I.620, L.621, L.624, A.661, L.665, H.669, E.674, I.678 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.624, B:I.678 Hydrogen bonds: B:R.617, B:R.617

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

MG.2: 3 residues within 4Å: Chain A: K.358, F.360 Chain D: A.2 No protein-ligand interaction detected (PLIP) MG.3: 5 residues within 4Å: Chain A: E.31, D.103, D.105, D.107 Chain C: T.11 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.103, A:D.105 MG.4: 1 residues within 4Å: Chain C: A.3 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain B: D.103, D.105, D.107 Chain F: T.11 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.103, B:D.105, B:D.105 MG.9: 2 residues within 4Å: Chain C: T.7, G.8 No protein-ligand interaction detected (PLIP) MG.12: 5 residues within 4Å: Chain E: T.6, A.7 Chain F: T.7, G.8, T.9 No protein-ligand interaction detected (PLIP)

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 2 residues within 4Å: Chain B: R.610, R.617 Ligand excluded by PLIP

2 x TNJ: 7-[(1S,5R)-1-amino-3-azabicyclo[3.1.0]hexan-3-yl]-4-(aminomethyl)-1-cyclopropyl-3,6-difluoro-8-methylquinolin-2(1H)-one(Non-covalent)

TNJ.10: 9 residues within 4Å: Chain A: R.364 Chain B: K.54, G.55, E.73, S.325 Chain D: G.1 Chain E: C.4, A.5 Chain F: T.11 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:K.54 Hydrogen bonds: B:E.73, A:R.364, A:R.364 Halogen bonds: B:S.325 TNJ.11: 10 residues within 4Å: Chain A: K.54, G.55, E.73, S.325 Chain B: R.364 Chain C: A.10, T.11 Chain D: C.4, A.5 Chain E: G.1 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:K.54 Hydrogen bonds: A:E.73, A:E.73, B:R.364, B:R.364

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Skepper, C.K. et al., Topoisomerase Inhibitors Addressing Fluoroquinolone Resistance in Gram-Negative Bacteria. J.Med.Chem. (2020)

Release Date

2020-07-15

Peptides

DNA topoisomerase 4 subunit B,DNA topoisomerase (ATP-hydrolyzing) chimera: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
H

DNA topoisomerase 4 subunit B,DNA topoisomerase (ATP-hydrolyzing) chimera

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