SMTL ID : 6eng.1

Crystal structure of the 43K ATPase domain of Escherichia coli gyrase B in complex with an aminocoumarin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

5 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 3 residues within 4Å: Chain A: R.195, Y.231, K.234 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.231, A:Y.231, A:Y.231 Water bridges: A:R.195, A:R.195 Salt bridges: A:R.195, A:K.234 PO4.2: 3 residues within 4Å: Chain A: H.67, R.171, K.211 7 PLIP interactions: 7 interactions with chain A Water bridges: A:D.69, A:R.171, A:K.211, A:K.211 Salt bridges: A:H.67, A:R.171, A:K.211 PO4.10: 3 residues within 4Å: Chain B: R.195, Y.231, K.234 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.195, B:R.195 Salt bridges: B:R.195, B:K.234 PO4.11: 3 residues within 4Å: Chain B: H.67, R.171, K.211 8 PLIP interactions: 8 interactions with chain B Water bridges: B:A.68, B:D.69, B:R.171, B:R.171, B:K.211 Salt bridges: B:H.67, B:R.171, B:K.211 PO4.12: 2 residues within 4Å: Chain B: K.226, Y.245 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.245, B:Y.245 Salt bridges: B:K.226

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 10 residues within 4Å: Chain A: E.267, N.268, I.269, Y.270, C.271, Q.278, R.279, G.281, L.285, R.289 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.267, A:I.269, A:C.271, A:Q.278, A:R.289 Water bridges: A:I.269

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 2 residues within 4Å: Chain A: R.207, H.218 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain B: R.207, H.218 Ligand excluded by PLIP

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

NA.5: 5 residues within 4Å: Chain A: I.276, P.277, T.339, K.340, D.341 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.339

3 x K: POTASSIUM ION(Non-covalent)

K.6: 3 residues within 4Å: Chain A: G.105, K.106, D.108 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:K.106, H2O.2 K.7: 2 residues within 4Å: Chain A: N.274, I.276 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:N.274, H2O.4, H2O.4, H2O.5 K.8: 1 residues within 4Å: Chain A: Y.245 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Y.245, H2O.6, H2O.7

1 x BHW: Coumermycin A1(Non-covalent)

BHW.9: 36 residues within 4Å: Chain A: V.46, N.49, A.50, E.53, V.74, D.76, R.79, G.80, I.81, I.97, G.104, F.107, D.108, K.113, V.123, R.139, T.168 Chain B: V.46, N.49, A.50, E.53, V.74, D.76, R.79, G.80, I.81, P.82, I.97, G.104, F.107, D.108, K.113, V.123, R.139, T.168, V.170 37 PLIP interactions: 20 interactions with chain A, 17 interactions with chain B Hydrophobic interactions: A:V.46, A:N.49, A:V.74, A:I.81, A:I.97, A:F.107, A:V.123, B:V.46, B:N.49, B:A.50, B:V.74, B:I.81, B:I.97, B:F.107, B:V.123, B:V.170 Hydrogen bonds: A:N.49, A:D.76, A:R.79, A:K.113, B:D.76 Water bridges: A:N.49, A:E.53, A:R.79, A:F.107, A:D.108, B:D.52, B:R.79, B:D.108 Salt bridges: A:R.79, A:K.113, A:R.139, B:R.79, B:K.113, B:R.139 pi-Cation interactions: A:R.79, B:R.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vanden Broeck, A. et al., Structural Basis for DNA Gyrase Interaction with Coumermycin A1. J.Med.Chem. (2019)

Release Date

2019-04-10

Peptides

DNA gyrase subunit B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA gyrase subunit B