SMTL ID : 6qtk.1

2.31A structure of gepotidacin with S.aureus DNA gyrase and doubly nicked DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

hetero-2-2-mer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: E.27, D.100 Chain E: G.8, G.9 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.27, A:D.100, H2O.1, H2O.2, H2O.29 MN.5: 4 residues within 4Å: Chain C: E.27, D.100 Chain F: G.8, G.9 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.27, C:D.100, H2O.15, H2O.15

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain B: K.65, R.68 Chain D: G.71, D.72, G.75, K.76 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:R.68, D:G.71 Water bridges: D:G.75 GOL.4: 8 residues within 4Å: Chain B: F.96, S.111, M.112, G.114, Q.266, V.267, N.268 Chain E: C.4 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.111, B:G.114, B:Q.266 Water bridges: B:Q.94, B:F.96, B:S.97, B:Q.266, B:N.268, B:R.271 GOL.6: 6 residues within 4Å: Chain D: A.31, P.43, R.46, R.47, E.155, P.156 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.46, D:E.155 Water bridges: D:V.30, D:R.47 GOL.7: 4 residues within 4Å: Chain D: E.250, G.254, R.255, Q.256 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.250, D:G.254, D:G.254 GOL.8: 5 residues within 4Å: Chain D: D.147, G.151, N.152, E.153, R.154 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.151 Water bridges: D:E.153, D:E.153 GOL.9: 4 residues within 4Å: Chain A: E.143 Chain D: Y.63, Q.106, E.124 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:Q.106, D:E.124, A:E.143, A:E.143 GOL.10: 6 residues within 4Å: Chain B: S.83 Chain E: A.7, G.8, G.9, T.10 Chain F: C.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.83 Water bridges: B:G.81 GOL.11: 2 residues within 4Å: Chain E: G.18 Chain F: G.2 No protein-ligand interaction detected (PLIP)

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain B: Y.321, K.322, T.324, Q.327 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.324, B:Q.327, B:Q.327

1 x JHN: (3~{R})-3-[[4-(3,4-dihydro-2~{H}-pyrano[2,3-c]pyridin-6-ylmethylamino)piperidin-1-yl]methyl]-1,4,7-triazatricyclo[6.3.1.0^{4,12}]dodeca-6,8(12),9-triene-5,11-dione(Non-covalent)

JHN.12: 11 residues within 4Å: Chain B: A.67, M.74, D.82, M.120 Chain D: A.67, D.82, M.120 Chain E: T.10, A.11 Chain F: T.10, A.11 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.67 Hydrogen bonds: B:D.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gibson, E.G. et al., Mechanistic and Structural Basis for the Actions of the Antibacterial Gepotidacin against Staphylococcus aureus Gyrase. Acs Infect Dis. (2019)

Release Date

2019-03-13

Peptides

DNA gyrase subunit B: AC
DNA gyrase subunit A: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

C
D

B
A

D
C

DNA gyrase subunit B

DNA gyrase subunit A

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