SMTL ID : 6ttg.1 (1 other biounit)

Crystal structure of the ATP binding domain of S. aureus GyrB complexed with LMD62

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x NWK: 2-[[3,4-bis(chloranyl)-5-methyl-1~{H}-pyrrol-2-yl]carbonylamino]-4-(2-morpholin-4-ylethoxy)-1,3-benzothiazole-6-carboxylic acid(Non-covalent)

NWK.1: 13 residues within 4Å: Chain A: I.52, N.55, S.56, E.59, D.82, R.85, G.86, I.87, P.88, I.103, R.122, T.151, I.153 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.52, A:R.85, A:P.88, A:I.153 Hydrogen bonds: A:D.82, A:T.151 Water bridges: A:N.55, A:E.59 Salt bridges: A:R.85, A:R.122

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: R.178, E.179, F.182 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.178

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

MPD.3: 5 residues within 4Å: Chain A: Y.119, H.121, I.126, V.152 Ligands: MPD.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.119, A:Y.119, A:I.126, A:V.152 Hydrogen bonds: A:H.121 MPD.4: 9 residues within 4Å: Chain A: T.81, D.82, H.121, K.148, T.149, G.150, V.152 Ligands: MPD.3, MPD.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.81, A:K.148 Hydrogen bonds: A:T.149 MPD.5: 3 residues within 4Å: Chain A: Q.67, T.81 Ligands: MPD.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.67 Hydrogen bonds: A:Q.67

1 x CA: CALCIUM ION(Non-covalent)

CA.6: 1 residues within 4Å: Chain A: D.58 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.58, H2O.3, H2O.4

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

CL.7: 5 residues within 4Å: Chain A: P.88, V.89, D.90, R.122, N.123 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Durcik, M. et al., New dual ATP-competitive inhibitors of bacterial DNA gyrase and topoisomerase IV active against ESKAPE pathogens. Eur.J.Med.Chem. (2021)

Release Date

2020-12-30

Peptides

DNA gyrase subunit B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA gyrase subunit B

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