SMTL ID : 5npk.2 (1 other biounit)

1.98A STRUCTURE OF THIOPHENE1 WITH S.AUREUS DNA GYRASE AND DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 2 residues within 4Å: Chain A: D.100, D.102 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.100, A:D.102, H2O.2, H2O.13, H2O.14, H2O.48 MN.10: 3 residues within 4Å: Chain B: E.27, D.100, D.102 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.100, B:D.102, H2O.26, H2O.33, H2O.35, H2O.51 MN.14: 1 residues within 4Å: Chain B: H.591 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.591

3 x 94H: ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-4-(1~{H}-pyrrolo[2,3-b]pyridin-3-yl)thiophene-2-carboxamide(Non-covalent)

94H.2: 10 residues within 4Å: Chain A: R.188, I.191, E.192, A.195, M.228, V.232, M.380, I.537, R.543, P.544 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.195, A:I.537, A:R.543, A:P.544 Hydrogen bonds: A:R.188, A:P.544 Water bridges: A:R.543, A:R.543 94H.9: 9 residues within 4Å: Chain A: R.586, I.587, D.590, H.591, E.594, R.615, F.616, K.617 Ligands: 9JN.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:R.586, A:I.587, A:E.594, A:F.616, A:F.616 Hydrogen bonds: A:K.617 pi-Stacking: A:H.591 94H.11: 11 residues within 4Å: Chain B: R.188, I.191, E.192, A.195, M.228, I.231, V.232, M.380, I.537, R.543, P.544 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:A.195, B:I.537, B:P.544 Hydrogen bonds: B:R.188, B:P.544

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: M.276, P.281, H.282, G.283 Chain B: R.323, F.324 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.323 Water bridges: A:E.143, A:E.143 GOL.4: 6 residues within 4Å: Chain A: P.245, R.248, R.249, I.348, E.357, P.358 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.248, A:P.358 Water bridges: A:V.232, A:V.232, A:E.357 GOL.5: 6 residues within 4Å: Chain A: R.323, F.324 Chain B: M.276, P.281, H.282, G.283 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.267, A:R.323, B:P.281, B:H.282 GOL.12: 6 residues within 4Å: Chain B: S.37, G.38, R.39, D.40, D.147, W.150 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.39, B:D.147 GOL.13: 6 residues within 4Å: Chain B: P.245, R.248, R.249, I.348, E.357, P.358 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.245, B:R.248 GOL.16: 4 residues within 4Å: Chain A: R.50, G.51 Chain C: G.8, G.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.50, A:R.50 Water bridges: A:S.285, A:S.285, A:S.285

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

SO4.6: 4 residues within 4Å: Chain A: R.630 Chain B: D.628, R.630, R.633 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.633 Water bridges: B:R.630, A:R.630 Salt bridges: B:R.630, A:R.630

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

NA.7: 4 residues within 4Å: Chain A: Y.523, K.524, T.526, Q.529 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.526, A:Q.529, A:Q.529

2 x 9JN: ~{N}-[(1~{S})-2-azanyl-1-phenyl-ethyl]-4-(1~{H}-pyrrolo[2,3-b]pyridin-3-yl)thiophene-2-carboxamide(Non-covalent)

9JN.8: 9 residues within 4Å: Chain A: R.586, I.587, D.590, H.591, E.594, R.615, F.616, K.617 Ligands: 94H.9 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:D.590, A:E.594, A:F.616, A:F.616 Hydrogen bonds: A:R.586, A:R.615, A:K.617 pi-Stacking: A:H.591 9JN.15: 3 residues within 4Å: Chain A: R.60 Chain C: A.1 Chain D: T.20 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.60 Water bridges: A:R.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chan, P.F. et al., Thiophene antibacterials that allosterically stabilize DNA-cleavage complexes with DNA gyrase. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-07-12

Peptides

DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
b

B
d

DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit A

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