SMTL ID : 6xg4.1

X-ray structure of Escherichia coli dihydrofolate reductase L28R mutant in complex with trimethoprim

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.1: 30 residues within 4Å: Chain A: A.6, A.7, I.14, G.15, M.16, N.18, A.19, M.20, W.22, G.43, R.44, H.45, T.46, L.62, S.63, S.64, Q.65, K.76, S.77, V.78, I.94, G.95, G.96, G.97, R.98, V.99, Y.100, Q.102, T.123 Ligands: TOP.3 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:T.46 Hydrogen bonds: A:A.7, A:I.14, A:M.16, A:N.18, A:A.19, A:R.44, A:H.45, A:H.45, A:T.46, A:T.46, A:S.49, A:S.49, A:S.64, A:Q.65, A:V.78, A:G.96, A:G.97, A:R.98, A:R.98, A:R.98, A:V.99, A:Q.102, A:Q.102 Water bridges: A:R.44, A:R.44, A:H.45, A:S.64, A:R.98, A:T.123, A:T.123 Salt bridges: A:R.44, A:H.45

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: D.116, S.148, H.149, S.150 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.149, A:S.150, A:S.150 Water bridges: A:D.116, A:S.150

1 x TOP: TRIMETHOPRIM(Non-covalent)

TOP.3: 13 residues within 4Å: Chain A: I.5, A.6, A.7, M.20, D.27, R.28, F.31, S.49, I.50, I.94, Y.100, T.113 Ligands: NDP.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.31, A:F.31 Hydrogen bonds: A:S.49, A:I.94, A:Y.100, A:T.113, A:T.113 Water bridges: A:A.6, A:M.20 Salt bridges: A:D.27 pi-Stacking: A:F.31

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

CL.4: 2 residues within 4Å: Chain A: R.98, Q.102 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Manna, M.S. et al., A trimethoprim derivative impedes antibiotic resistance evolution. Nat Commun (2021)

Release Date

2021-03-24

Peptides

Dihydrofolate reductase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydrofolate reductase