SMTL ID : 5cdm.1

2.5A structure of QPT-1 with S.aureus DNA gyrase and DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-mer

Ligands

2 x DG- DA- DG- DC- DG- DT- DA- DC: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')(Non-covalent)

DG-DA-DG-DC-DG-DT-DA-DC.1: 31 residues within 4Å: Chain A: E.20, G.44, K.45, D.97, I.101 Chain B: R.25, K.35, V.37, H.38, H.71, H.73, G.74, S.77, A.81, R.84, S.165, G.166, I.167, Q.259, N.261, R.264 Chain D: Y.115 Chain F: G.5, T.6, A.7, C.8, G.9, C.10, T.11 Ligands: MN.3, 54Q.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.43 DG-DA-DG-DC-DG-DT-DA-DC.2: 30 residues within 4Å: Chain B: Y.115 Chain C: E.20, G.44, K.45, D.97, I.101 Chain D: R.25, K.35, P.36, V.37, H.38, H.71, H.73, G.74, S.77, E.80, A.81, R.84, S.165, I.167, Q.259, R.264 Chain E: G.5, T.6, A.7, C.8, G.9, C.10, T.11 Ligands: 54Q.9 15 PLIP interactions: 10 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:K.45, C:K.45, C:N.48, C:N.48, D:G.170 Salt bridges: C:K.51, C:K.51, C:R.56, C:R.56, C:H.100, C:R.180, D:R.230 Hydrophobic interactions: D:I.167 Water bridges: D:R.230, D:R.230

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

MN.3: 3 residues within 4Å: Chain A: D.93, D.95 Ligands: DG-DA-DG-DC-DG-DT-DA-DC.1 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.93, A:D.95, H2O.1, H2O.1, H2O.2 MN.8: 2 residues within 4Å: Chain C: D.93, D.95 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.93, C:D.95, H2O.6, H2O.7, H2O.7

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: N.59, N.60, N.61, E.62 Chain F: G.5, T.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.61, A:N.61 GOL.7: 8 residues within 4Å: Chain B: A.24, P.36, R.39, R.40, I.139, E.148, P.149, S.150 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.39, B:R.40 Water bridges: B:E.148

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

SO4.5: 4 residues within 4Å: Chain B: N.305, S.307, V.308, N.311 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.305, B:S.307, B:N.311

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

NA.6: 4 residues within 4Å: Chain B: Y.314, T.317, P.318, Q.320 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.315, B:T.317, B:Q.320

2 x 54Q: (2R,4S,4aS)-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',6'(1'H,3'H)-trione(Non-covalent)

54Q.9: 11 residues within 4Å: Chain B: R.114, Y.115 Chain C: G.21, D.22, R.43, G.44 Chain D: S.76 Chain E: C.4, G.5 Chain F: G.1 Ligands: DA-DG-DC-DG-DT-DA-DC.2 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.22 Water bridges: C:G.44, C:G.44 54Q.11: 11 residues within 4Å: Chain A: G.21, D.22, R.43, G.44 Chain B: S.76 Chain D: R.114, Y.115 Chain E: G.1 Chain F: C.4, G.5 Ligands: DG-DA-DG-DC-DG-DT-DA-DC.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.22

1 x DT: THYMIDINE-5'-MONOPHOSPHATE(Non-functional Binders)

DT.10: 2 residues within 4Å: Chain B: S.232 Chain F: T.11 No protein-ligand interaction detected (PLIP)

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 B,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 B

DNA gyrase subunit A

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