SMTL ID : 5cdo.1 (1 other biounit)

3.15A structure of QPT-1 with S.aureus DNA gyrase and DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.15 Å

Oligo State

hetero-oligomer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: R.421 Chain C: D.419, R.421, R.424 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.424 Salt bridges: C:R.421, A:R.421

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

NA.2: 4 residues within 4Å: Chain A: Y.314, K.315, T.317, Q.320 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.317 NA.5: 4 residues within 4Å: Chain C: G.144, N.145, E.146, R.147 No protein-ligand interaction detected (PLIP) NA.6: 5 residues within 4Å: Chain C: Y.314, K.315, T.317, P.318, Q.320 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.314, C:T.317

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: P.36, R.39, R.40, I.139, E.148, P.149, S.150 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.39, A:P.149, A:P.149 GOL.8: 6 residues within 4Å: Chain D: N.58, N.59, N.60, E.61 Chain E: G.13, T.14 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.60, D:N.60 GOL.9: 8 residues within 4Å: Chain A: S.289, L.290 Chain D: S.29, G.30, R.31, D.32, D.139, W.142 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.31, D:W.142

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

MN.4: 4 residues within 4Å: Chain B: E.19, D.92, D.94 Chain E: C.8 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.92, B:D.94, H2O.1, H2O.1, H2O.1 MN.7: 2 residues within 4Å: Chain D: D.92, D.94 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.92, D:D.94, H2O.1, H2O.1, H2O.1

1 x 53M: (2R,4S,4aS)-4',6'-dihydroxy-2,4-dimethyl-8-nitro-1,2,4,4a-tetrahydro-2'H,6H-spiro[1,4-oxazino[4,3-a]quinoline-5,5'-pyrimidin]-2'-one

53M.10: 11 residues within 4Å: Chain A: S.76 Chain B: G.20, D.21, R.42, G.43 Chain C: R.114, Y.115 Chain E: C.8, G.9 Chain F: C.12, G.13 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.42 Hydrogen bonds: B:D.21

1 x 53L: (2R,4S,4aS,5S)-6'-hydroxy-2,4-dimethyl-8-nitro-1,2,4,4a-tetrahydro-2'H,6H-spiro[1,4-oxazino[4,3-a]quinoline-5,5'-pyrimidine]-2',4'(3'H)-dione

53L.11: 11 residues within 4Å: Chain A: R.114, Y.115 Chain C: S.76 Chain D: G.20, D.21, R.42, G.43 Chain E: C.12, G.13 Chain F: C.8, G.9 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.21, D:D.21, D:G.43 Water bridges: D:G.20, D:G.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chan, P.F. et al., Structural basis of DNA gyrase inhibition by antibacterial QPT-1, anticancer drug etoposide and moxifloxacin. Nat Commun (2015)

Release Date

2015-12-16

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

DNA gyrase subunit A

DNA gyrase subunit B,DNA gyrase subunit B

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