SMTL ID : 2y3p.1

Crystal structure of N-terminal domain of GyrA with the antibiotic simocyclinone D8

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.62 Å

Oligo State

homo-tetramer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain D: R.120 Ligands: SM8.6 No protein-ligand interaction detected (PLIP) MG.2: 2 residues within 4Å: Chain C: R.46 Ligands: SM8.6 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain C: R.120 Ligands: SM8.3 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain D: R.46 Ligands: SM8.3 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain B: R.120 Ligands: SM8.12 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain A: R.46 Ligands: SM8.12 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain A: R.120 Ligands: SM8.9 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain B: R.46 Ligands: SM8.9 No protein-ligand interaction detected (PLIP)

4 x SM8: SIMOCYCLINONE D8(Non-covalent)

SM8.3: 21 residues within 4Å: Chain A: L.40, K.41, H.44, T.87, R.90, M.91, L.97, L.101, N.164, N.168, G.169, A.174 Chain C: R.120 Chain D: V.27, R.31, R.46, H.77, H.79, D.81 Ligands: MG.4, MG.5 18 PLIP interactions: 6 interactions with chain D, 11 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: D:V.27, D:D.81, A:A.174 Hydrogen bonds: D:R.31, D:R.46, D:R.46, A:T.87, A:R.90, A:R.90, A:N.164, C:R.120 pi-Stacking: D:H.79, A:H.44 Water bridges: A:K.41 Salt bridges: A:K.41, A:H.44 pi-Cation interactions: A:H.44 Halogen bonds: A:N.168 SM8.6: 18 residues within 4Å: Chain B: L.40, H.44, R.90, M.91, L.101, N.164, N.168, G.169, S.171 Chain C: V.27, R.31, R.46, H.77, H.79, D.81 Chain D: R.120 Ligands: MG.1, MG.2 13 PLIP interactions: 6 interactions with chain B, 6 interactions with chain C, 1 interactions with chain D Hydrogen bonds: B:R.90, B:N.164, C:R.31, C:R.46, C:R.46, D:R.120 Water bridges: B:S.171 pi-Stacking: B:H.44, C:H.79 Halogen bonds: B:N.168, B:G.169 Hydrophobic interactions: C:H.79, C:D.81 SM8.9: 21 residues within 4Å: Chain A: R.120 Chain B: V.27, R.31, R.46, H.77, H.79, D.81 Chain C: L.40, K.41, H.44, T.87, R.90, M.91, L.97, L.101, N.164, N.168, G.169, A.174 Ligands: MG.10, MG.11 18 PLIP interactions: 6 interactions with chain B, 11 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: B:V.27, B:D.81, C:A.174 Hydrogen bonds: B:R.31, B:R.46, B:R.46, C:T.87, C:R.90, C:R.90, C:N.164, A:R.120 pi-Stacking: B:H.79, C:H.44 Water bridges: C:K.41 Salt bridges: C:K.41, C:H.44 pi-Cation interactions: C:H.44 Halogen bonds: C:N.168 SM8.12: 18 residues within 4Å: Chain A: V.27, R.31, R.46, H.77, H.79, D.81 Chain B: R.120 Chain D: L.40, H.44, R.90, M.91, L.101, N.164, N.168, G.169, S.171 Ligands: MG.7, MG.8 13 PLIP interactions: 6 interactions with chain A, 6 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: A:H.79, A:D.81 Hydrogen bonds: A:R.31, A:R.46, A:R.46, D:R.90, D:N.164, B:R.120 pi-Stacking: A:H.79, D:H.44 Water bridges: D:S.171 Halogen bonds: D:N.168, D:G.169

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Edwards, M.J. et al., A Crystal Structure of the Bifunctional Antibiotic Simocyclinone D8, Bound to DNA Gyrase. Science (2009)

Release Date

2010-12-29

Peptides

DNA GYRASE SUBUNIT A: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

DNA GYRASE SUBUNIT A