SMTL ID : 7nae.1

Crystal structure of Escherichia coli dihydrofolate reductase in complex with TRIMETHOPRIM

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

2 x TOP: TRIMETHOPRIM(Non-covalent)

TOP.1: 13 residues within 4Å: Chain A: I.5, A.6, A.7, M.16, W.22, D.27, L.28, F.31, I.50, L.54, I.94, Y.100, T.113 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.31, A:F.31, A:I.50 Hydrogen bonds: A:I.5, A:A.6, A:A.7, A:T.113 Water bridges: A:A.6 Salt bridges: A:D.27 pi-Stacking: A:F.31 TOP.7: 13 residues within 4Å: Chain B: I.5, A.6, A.7, M.16, W.22, D.27, L.28, F.31, I.50, L.54, I.94, Y.100, T.113 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.31, B:F.31, B:I.50 Hydrogen bonds: B:I.5, B:A.6, B:A.7, B:Y.100, B:T.113 Water bridges: B:A.6 Salt bridges: B:D.27 pi-Stacking: B:F.31

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

SO4.2: 5 residues within 4Å: Chain A: K.32, R.52, L.54, P.55, R.57 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.32, A:R.52, A:R.57 SO4.3: 7 residues within 4Å: Chain A: L.104, D.127, Y.128, E.129, D.132, W.133, R.158 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.129, A:D.132 Salt bridges: A:R.158 SO4.4: 5 residues within 4Å: Chain A: R.12 Chain B: D.116, A.143, H.149, S.150 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.149, B:S.150 Water bridges: B:A.143, B:A.143 Salt bridges: A:R.12 SO4.5: 5 residues within 4Å: Chain A: R.44, S.63, S.64, Q.65, R.98 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.64, A:R.98 Water bridges: A:L.62, A:S.64 Salt bridges: A:R.44 SO4.6: 8 residues within 4Å: Chain A: M.16, G.43, R.44, H.45, T.46, G.96, R.98, V.99 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.43, A:R.44, A:H.45, A:T.46, A:G.96, A:G.96, A:V.99 Water bridges: A:R.98 Salt bridges: A:H.45, A:R.98 SO4.8: 5 residues within 4Å: Chain B: K.32, R.52, L.54, P.55, R.57 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:K.32, B:R.52, B:R.57 SO4.9: 7 residues within 4Å: Chain B: L.104, D.127, Y.128, E.129, D.132, W.133, R.158 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.129, B:D.132, B:D.132 Salt bridges: B:R.158 SO4.10: 5 residues within 4Å: Chain A: D.116, A.143, H.149, S.150 Chain B: R.12 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Salt bridges: B:R.12 Hydrogen bonds: A:S.150 Water bridges: A:A.143, A:A.143 SO4.11: 5 residues within 4Å: Chain B: R.44, S.63, S.64, Q.65, R.98 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.64, B:R.98 Water bridges: B:L.62, B:S.64 Salt bridges: B:R.44 SO4.12: 8 residues within 4Å: Chain B: M.16, G.43, R.44, H.45, T.46, G.96, R.98, V.99 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.43, B:R.44, B:H.45, B:T.46, B:T.46, B:G.96, B:G.96, B:V.99 Water bridges: B:R.98 Salt bridges: B:H.45, B:R.98

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krucinska, J. et al., Structure-guided functional studies of plasmid-encoded dihydrofolate reductases reveal a common mechanism of trimethoprim resistance in Gram-negative pathogens. Commun Biol (2022)

Release Date

2022-06-29

Peptides

Dihydrofolate reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Dihydrofolate reductase