SMTL ID : 5d7c.2 (1 other biounit)

Crystal structure of the ATP binding domain of S. aureus GyrB complexed with a ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

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

MPD.1: 9 residues within 4Å: Chain A: T.81, D.82, N.83, H.121, K.148, T.149, G.150, T.151 Ligands: MPD.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.81, A:K.148 Hydrogen bonds: A:T.149 MPD.2: 5 residues within 4Å: Chain A: Y.119, H.121, I.126, V.152 Ligands: MPD.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.119, A:Y.119, A:Y.119, A:I.126 Water bridges: A:K.79

1 x 57W: 1-ethyl-3-[1-(pyridin-2-yl)-6-(pyridin-3-yl)-1H-pyrrolo[3,2-b]pyridin-3-yl]urea(Non-covalent)

57W.3: 14 residues within 4Å: Chain A: I.52, N.55, S.56, E.59, V.80, D.82, R.85, G.86, I.87, P.88, I.103, R.122, T.151, I.153 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.80, A:I.103, A:I.103, A:I.153 Hydrogen bonds: A:N.55, A:D.82, A:D.82, A:R.122 Water bridges: A:R.122, A:R.122, A:T.151, A:T.151 pi-Cation interactions: A:R.85

7 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 1 residues within 4Å: Chain A: D.58 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.58, H2O.1, H2O.1, H2O.2, H2O.4 MG.5: 1 residues within 4Å: Chain A: E.142 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.142, A:E.142, H2O.6, H2O.6 MG.6: 1 residues within 4Å: Chain A: L.61 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:L.61, H2O.4, H2O.5, H2O.7 MG.7: 2 residues within 4Å: Chain A: N.55 Ligands: MG.10 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain A: N.83, G.84, T.149 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:N.83, A:T.149, A:T.149, H2O.4, H2O.4 MG.9: 2 residues within 4Å: Chain A: G.186, H.206 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.186, A:H.206, H2O.3, H2O.5 MG.10: 2 residues within 4Å: Chain A: D.54 Ligands: MG.7 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, J. et al., Discovery of Azaindole Ureas as a Novel Class of Bacterial Gyrase B Inhibitors. J.Med.Chem. (2015)

Release Date

2015-11-25

Peptides

DNA gyrase subunit B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

DNA gyrase subunit B

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