SMTL ID : 5d7d.2 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

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

MPD.1: 6 residues within 4Å: Chain A: T.81, D.82, H.121, K.148, G.150 Ligands: MPD.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.81, A:K.148 Water bridges: A:T.149 MPD.2: 4 residues within 4Å: Chain A: Y.119, H.121, 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:V.152 Water bridges: A:K.79

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

CL.3: 5 residues within 4Å: Chain A: P.88, V.89, D.90, R.122, N.123 Ligand excluded by PLIP

3 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 1 residues within 4Å: Chain A: N.55 No protein-ligand interaction detected (PLIP) MG.5: 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.3, H2O.5 MG.6: 2 residues within 4Å: Chain A: G.186, H.206 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:G.186, A:H.206, H2O.3, H2O.5, H2O.5

1 x 57X: 7-propyl-3-[2-(pyridin-3-yl)-1,3-thiazol-5-yl]-1,7-dihydro-6H-pyrazolo[3,4-b]pyridin-6-one(Non-covalent)

57X.7: 13 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, R.122, T.151, I.153 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:I.52, A:N.55, A:V.80, A:I.87, A:I.87, A:P.88, A:T.151, A:I.153 Hydrogen bonds: A:N.55, A:D.82, A:R.122, A:R.122 Water bridges: A:E.59, A:R.85, A:T.151, A:T.151 pi-Cation interactions: A:R.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, J. et al., Discovery of Indazole Derivatives as a Novel Class of Bacterial Gyrase B Inhibitors. Acs Med.Chem.Lett. (2015)

Release Date

2015-11-11

Peptides

DNA gyrase subunit B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

DNA gyrase subunit B

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