SMTL ID : 4plb.1

Crystal Structure of S.A. gyrase-AM8191 complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.69 Å

Oligo State

homo-dimer

Ligands

1 x 31N: 6-[({(1r,4S)-1-[(1S)-2-(3-fluoro-6-methoxy-1,5-naphthyridin-4-yl)-1-hydroxyethyl]-2-oxabicyclo[2.2.2]oct-4-yl}amino)methyl]-2H-pyrido[3,2-b][1,4]oxazin-3(4H)-one(Non-covalent)

31N.1: 13 residues within 4Å: Chain A: G.10, C.11 Chain B: G.10, C.11 Chain C: A.269, G.273, M.276, D.284, M.322 Chain D: A.269, G.273, M.276, D.284 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:D.284 Hydrogen bonds: C:D.284

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

SO4.2: 3 residues within 4Å: Chain C: R.630, R.633 Chain D: R.630 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:R.633 Salt bridges: C:R.630, D:R.630 SO4.4: 3 residues within 4Å: Chain C: R.630 Chain D: R.630, R.633 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Salt bridges: C:R.630, D:R.630, D:R.633 SO4.5: 4 residues within 4Å: Chain D: R.457, T.491, R.510, K.511 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.511 Salt bridges: D:R.457

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 4 residues within 4Å: Chain A: G.8, G.9 Chain C: E.27, D.100 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.27, C:D.100, H2O.2, H2O.2 MN.6: 5 residues within 4Å: Chain B: G.8, G.9 Chain D: E.27, D.100, D.102 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.27, D:D.100, H2O.3, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, S.B. et al., Oxabicyclooctane-linked novel bacterial topoisomerase inhibitors as broad spectrum antibacterial agents. Acs Med.Chem.Lett. (2014)

Release Date

2014-06-18

Peptides

Chimera protein of DNA gyrase subunits B and A: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
B

D
D

Chimera protein of DNA gyrase subunits B and A

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