SMTL ID : 8bp2.1

2.8A STRUCTURE OF ZOLIFLODACIN WITH S.AUREUS DNA GYRASE AND DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-2-2-mer

Ligands

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: N.59, N.60 Chain H: G.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.60 GOL.3: 3 residues within 4Å: Chain B: N.312, S.314, N.318 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.312, B:S.314 GOL.5: 6 residues within 4Å: Chain B: P.43, R.46, R.47, E.155, P.156, S.157 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.43, B:R.46, B:S.157 Water bridges: B:R.46 GOL.6: 4 residues within 4Å: Chain A: R.180 Chain B: M.178, I.335, P.342 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.180, B:L.344 GOL.7: 5 residues within 4Å: Chain B: V.247, E.249, V.259, T.261, R.302 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.249, B:E.249, B:R.302, B:R.302 GOL.11: 4 residues within 4Å: Chain D: M.112, G.114, Q.266, V.267 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:M.112 GOL.13: 4 residues within 4Å: Chain F: G.10 Chain H: G.9, G.10, C.11 No protein-ligand interaction detected (PLIP)

3 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 2 residues within 4Å: Chain A: D.92, D.94 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.92, A:D.94, H2O.1, H2O.1, H2O.1, H2O.7 MN.8: 3 residues within 4Å: Chain C: E.19, D.92, D.94 6 PLIP interactions: 2 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.92, C:D.94, H2O.4, H2O.5, H2O.5, H2O.8 MN.9: 2 residues within 4Å: Chain D: H.389 Ligands: BTB.10 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.389

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 3 residues within 4Å: Chain B: Y.321, T.324, Q.327 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.324, B:Q.327, B:Q.327

1 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.10: 3 residues within 4Å: Chain D: D.388, H.389 Ligands: MN.9 No protein-ligand interaction detected (PLIP)

2 x R8U: Zoliflodacin(Non-covalent)

R8U.12: 11 residues within 4Å: Chain B: R.121 Chain C: G.20, D.21, R.42, G.43, N.60, E.61 Chain F: C.12, G.13 Chain G: C.8 Chain H: G.9 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:D.21 Water bridges: C:D.21, C:D.21, C:R.42, C:G.43, C:G.43 R8U.14: 10 residues within 4Å: Chain A: G.20, D.21, R.42, G.43, N.60, E.61 Chain E: C.8 Chain F: G.9 Chain H: C.12, G.13 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.42 Hydrogen bonds: A:D.21 Water bridges: A:R.42, A:R.42

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morgan, H. et al., A 2.8 angstrom Structure of Zoliflodacin in a DNA Cleavage Complex with Staphylococcus aureus DNA Gyrase. Int J Mol Sci (2023)

Release Date

2023-02-08

Peptides

DNA gyrase subunit B: AC
DNA gyrase subunit A: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
BBB

C
DDD

B
AAA

D
CCC

DNA gyrase subunit B

DNA gyrase subunit A

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