SMTL ID : 4kfg.1

The DNA Gyrase B ATP binding domain of Escherichia coli in complex with a small molecule inhibitor.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: P.66, T.67, G.68, R.123, E.124 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.67, A:G.68 Salt bridges: A:R.123 SO4.2: 7 residues within 4Å: Chain A: V.98, S.99, G.100, H.103 Chain B: G.100, R.177, L.184 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.100 Salt bridges: A:H.103, B:R.177 Water bridges: B:G.100, B:G.100, B:G.100 SO4.4: 5 residues within 4Å: Chain B: P.66, T.67, G.68, R.123, E.124 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.67, B:G.68, B:E.124 Salt bridges: B:R.123

2 x DOO: 6-fluoro-4-[(3aR,6aR)-hexahydropyrrolo[3,4-b]pyrrol-5(1H)-yl]-N-methyl-2-[(2-methylpyrimidin-5-yl)oxy]-9H-pyrimido[4,5-b]indol-8-amine(Non-covalent)

DOO.3: 13 residues within 4Å: Chain A: N.33, A.34, E.37, V.58, D.60, R.63, G.64, I.65, P.66, I.81, V.107, T.152, V.154 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:N.33, A:I.65, A:I.65, A:I.81, A:V.154 Hydrogen bonds: A:D.60, A:D.60, A:T.152 Water bridges: A:N.33, A:E.37, A:G.64, A:R.123 pi-Cation interactions: A:R.63 DOO.5: 15 residues within 4Å: Chain B: N.33, A.34, D.36, E.37, V.58, D.60, R.63, G.64, I.65, P.66, I.81, M.82, V.107, T.152, V.154 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:N.33, B:I.65, B:I.65, B:V.154 Hydrogen bonds: B:D.60, B:D.60, B:D.60, B:R.63 Water bridges: B:N.33, B:E.37, B:E.37, B:E.37, B:R.123, B:T.152, B:T.152 pi-Cation interactions: B:R.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tari, L.W. et al., A new class of type IIA topoisomerase inhibitors with broad-spectrum antibacterial activity. To be Published

Release Date

2014-01-15

Peptides

DNA gyrase subunit B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA gyrase subunit B

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