SMTL ID : 5npk.1 (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

2 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.5, H2O.10, H2O.15, H2O.48 MN.7: 2 residues within 4Å: Chain B: 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.25, H2O.38, H2O.38, H2O.50

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: 11 residues within 4Å: Chain A: R.188, I.191, E.192, A.195, M.228, I.231, V.232, M.380, I.537, R.543, P.544 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.195, A:I.537, A:P.544 Hydrogen bonds: A:R.188, A:P.544 Water bridges: A:R.543, A:R.543 94H.6: 7 residues within 4Å: Chain A: R.586, I.587, D.590, H.591, E.594, R.615, F.616 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.594, A:F.616, A:F.616 Hydrogen bonds: A:D.590 pi-Stacking: A:H.591 94H.9: 9 residues within 4Å: Chain B: R.188, I.191, E.192, A.195, M.228, M.380, I.537, R.543, P.544 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.195, B:I.537, B:P.544 Hydrogen bonds: B:R.188, B:P.544 Water bridges: B:P.544

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: R.50 Chain C: G.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.50, A:R.50 Water bridges: A:S.285, A:S.285 GOL.4: 5 residues within 4Å: Chain A: S.37, G.38, R.39, D.40, W.150 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.37 Water bridges: A:W.150 GOL.5: 7 residues within 4Å: Chain A: F.298, S.313, M.314, G.316, Q.468, V.469 Chain C: C.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.316 Water bridges: A:V.469, A:V.469, A:N.470 GOL.8: 5 residues within 4Å: Chain B: S.37, G.38, R.39, D.147, W.150 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:T.497 Hydrogen bonds: B:D.147 GOL.10: 8 residues within 4Å: Chain A: K.267, R.323, F.324 Chain B: E.143, M.276, P.281, H.282, G.283 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.282, A:K.267, A:K.267 Water bridges: B:P.281 GOL.11: 7 residues within 4Å: Chain B: A.233, P.245, R.248, R.249, I.348, E.357, P.358 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.248, B:P.358 Water bridges: B:V.232, B:R.248, B:R.249, B:E.357 GOL.12: 5 residues within 4Å: Chain B: Y.252, E.256, Y.279, E.355, R.356 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.252, B:Y.252, B:E.256, B:E.355, B:E.355, B:R.356

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

CL.13: 1 residues within 4Å: Chain B: H.591 Ligand excluded by PLIP

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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