SMTL ID : 6tck.2 (1 other biounit)

Crystal structure of the ATP binding domain of S. aureus GyrB complexed with ULD-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x N1N: 2-[[3,4-bis(chloranyl)-5-methyl-1~{H}-pyrrol-2-yl]carbonylamino]-4-phenylmethoxy-1,3-benzothiazole-6-carboxylic acid(Non-covalent)

N1N.1: 13 residues within 4Å: Chain A: N.55, S.56, E.59, D.82, R.85, G.86, I.87, P.88, A.99, I.103, R.122, T.151, I.153 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:R.85, A:P.88, A:P.88, A:A.99, A:I.103, A:T.151, A:I.153 Hydrogen bonds: A:D.82 Water bridges: A:E.59, A:R.85, A:R.122, A:R.122, A:T.151 Salt bridges: A:R.85, A:R.122 pi-Cation interactions: A:R.85

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

MPD.2: 9 residues within 4Å: Chain A: T.81, D.82, N.83, H.121, K.148, T.149, G.150, T.151 Ligands: MPD.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.81, A:K.148 Hydrogen bonds: A:T.149 MPD.3: 4 residues within 4Å: Chain A: Y.119, H.121, V.152 Ligands: MPD.2 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 IMD: IMIDAZOLE(Non-covalent)

IMD.4: 3 residues within 4Å: Chain A: Y.127, L.140, E.142 No protein-ligand interaction detected (PLIP)

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

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

1 x CA: CALCIUM ION(Non-covalent)

CA.6: 1 residues within 4Å: Chain A: E.202 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.202, H2O.2

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.7: 4 residues within 4Å: Chain A: D.75, N.76, K.156, T.166 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.76 Salt bridges: A:D.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nyerges, A. et al., Rational design of balanced dual-targeting antibiotics with limited resistance. Plos Biol. (2020)

Release Date

2020-09-23

Peptides

DNA gyrase subunit B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

DNA gyrase subunit B

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