SMTL ID : 5npp.1

2.22A STRUCTURE OF THIOPHENE2 AND GSK945237 WITH S.AUREUS DNA GYRASE AND DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.22 Å

Oligo State

homo-dimer

Ligands

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

DA-DG-DC-DC-DG-DT-DA-DG.1: 30 residues within 4Å: Chain A: E.27, R.50, G.51, K.52, D.104, I.108, R.234, K.244, V.246, H.247, H.280, H.282, G.283, S.286, R.293, S.374, I.376, Q.468, R.473 Chain B: R.323 Chain C: G.1 Chain D: C.5, T.6, A.7, C.8, G.9, G.10, C.11 Ligands: DMS.9, GOL.16 Protein-ligand interaction information (PLIP) not available DA-DG-DC-DC-DG-DT-DA-DG.2: 29 residues within 4Å: Chain A: R.323 Chain B: E.27, R.50, G.51, K.52, D.104, R.234, K.244, V.246, H.247, H.280, H.282, G.283, S.286, R.293, S.374, I.376, R.473 Chain C: C.5, T.6, A.7, C.8, G.9, G.10, C.11, T.12 Chain D: G.1 Ligands: GOL.14, GOL.18 Protein-ligand interaction information (PLIP) not available

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

MN.3: 2 residues within 4Å: Chain A: D.100, D.102 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.100, A:D.102, H2O.6, H2O.7, H2O.8, H2O.20 MN.10: 2 residues within 4Å: Chain B: D.100, D.102 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.100, B:D.102, H2O.18, H2O.21, H2O.32

2 x 94K: ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide(Non-covalent)

94K.4: 13 residues within 4Å: Chain A: R.188, I.191, E.192, A.195, Y.197, I.231, V.232, M.380, I.537, R.543, P.544, K.545, L.546 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.191, A:E.192, A:E.192, A:A.195, A:Y.197, A:I.231, A:I.537, A:R.543, A:P.544 Hydrogen bonds: A:R.188, A:E.192, A:P.544 94K.11: 11 residues within 4Å: Chain B: R.188, I.191, E.192, A.195, Y.197, I.231, V.232, M.380, R.543, P.544, L.546 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:I.191, B:E.192, B:E.192, B:A.195, B:Y.197, B:I.231, B:R.543, B:P.544 Hydrogen bonds: B:R.188, B:E.192 Water bridges: B:E.192, B:E.192, B:P.544

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: E.452, G.456, R.457, Q.458 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.456, A:R.457, A:Q.458 GOL.6: 6 residues within 4Å: Chain A: P.245, R.248, R.249, I.348, E.357, P.358 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.248, A:E.357, A:S.359 Water bridges: A:R.249 GOL.7: 7 residues within 4Å: Chain A: N.388, T.390, E.391, E.415, D.683, D.684, R.685 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.390, A:T.390, A:E.391, A:D.684, A:R.685 GOL.12: 7 residues within 4Å: Chain B: A.233, P.245, R.248, R.249, I.348, E.357, P.358 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.248, B:E.357 Water bridges: B:V.232, B:R.248, B:E.357 GOL.13: 4 residues within 4Å: Chain B: E.452, G.456, R.457, Q.458 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.456, B:R.457 Water bridges: B:R.453, B:G.456, B:Q.458 GOL.14: 6 residues within 4Å: Chain B: S.313, M.314, G.316, Q.468, N.470 Ligands: DA-DG-DC-DC-DG-DT-DA-DG.2 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.468 Water bridges: B:Q.296, B:F.298, B:V.469, B:N.470 GOL.15: 3 residues within 4Å: Chain B: I.587, D.590, H.591 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.590 GOL.16: 5 residues within 4Å: Chain A: S.285 Chain C: G.1, T.2 Ligands: DA-DG-DC-DC-DG-DT-DA-DG.1, DA-DG-DC-DC-DG-DT-DA-DG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.285 Water bridges: A:S.286 GOL.18: 6 residues within 4Å: Chain B: S.285 Chain C: C.5 Chain D: G.1, T.2 Ligands: DA-DG-DC-DC-DG-DT-DA-DG.2, DA-DG-DC-DC-DG-DT-DA-DG.2 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.285 Water bridges: B:S.285

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

NA.8: 4 residues within 4Å: Chain A: Y.523, K.524, T.526, Q.529 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.526, A:Q.529, A:Q.529

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.9: 6 residues within 4Å: Chain A: F.298, S.313, M.314, G.316, Q.468 Ligands: DA-DG-DC-DC-DG-DT-DA-DG.1 No protein-ligand interaction detected (PLIP)

1 x 6EJ: (1R)-1-[(4-{[(6,7-dihydro[1,4]dioxino[2,3-c]pyridazin-3-yl)methyl]amino}piperidin-1-yl)methyl]-9-fluoro-1,2-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-4-one(Non-covalent)

6EJ.17: 11 residues within 4Å: Chain A: A.269, D.284, M.322 Chain B: A.269, G.273, M.276, D.284 Chain C: T.2, A.3 Chain D: T.2, A.3 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:D.284, A:D.284

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chan, P.F. et al., Thiophene antibacterials that allosterically stabilize DNA-cleavage complexes with DNA gyrase. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-07-12

Peptides

DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit A