SMTL ID : 7reb.1

E. coli dihydrofolate reductase complexed with 5-(3-(7-(4-(aminomethyl)phenyl)benzo[d][1,3]dioxol-5-yl)but-1-yn-1-yl)-6-ethylpyrimidine-2,4-diamine (UCP1223)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 7 residues within 4Å: Chain A: G.43, R.44, H.45, T.46, G.96, R.98, V.99 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.43, A:G.43, A:H.45, A:T.46, A:T.46, A:G.96, A:V.99 Water bridges: A:R.44, A:G.97, A:R.98, A:R.98 Salt bridges: A:H.45, A:R.98 SO4.2: 5 residues within 4Å: Chain A: R.44, S.63, S.64, Q.65, R.98 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.63, A:S.64, A:Q.65 Water bridges: A:R.98 Salt bridges: A:R.44, A:R.98 SO4.3: 6 residues within 4Å: Chain A: L.104, Y.128, E.129, D.132, W.133, R.158 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.129, A:W.133 Salt bridges: A:R.158 SO4.4: 4 residues within 4Å: Chain A: R.12, H.114 Chain B: D.116, S.150 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.150, B:S.150, A:H.114 Water bridges: A:R.12 Salt bridges: A:R.12 SO4.5: 2 residues within 4Å: Chain A: D.79, K.106 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.79 Salt bridges: A:K.106 SO4.6: 2 residues within 4Å: Chain A: R.44, H.45 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.44, A:H.45 SO4.7: 1 residues within 4Å: Chain A: K.58 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.58, A:T.73 Salt bridges: A:K.58 SO4.9: 7 residues within 4Å: Chain B: G.43, R.44, H.45, T.46, G.96, R.98, V.99 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.43, B:G.43, B:H.45, B:T.46, B:G.96, B:V.99 Water bridges: B:R.44, B:G.97, B:R.98, B:R.98 Salt bridges: B:H.45, B:R.98 SO4.10: 5 residues within 4Å: Chain B: R.44, S.63, S.64, Q.65, R.98 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.63, B:S.64, B:Q.65 Water bridges: B:R.98 Salt bridges: B:R.44, B:R.98 SO4.11: 6 residues within 4Å: Chain B: L.104, 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:W.133 Salt bridges: B:R.158 SO4.12: 4 residues within 4Å: Chain A: D.116, S.150 Chain B: R.12, H.114 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:H.114, A:D.116, A:S.150, A:S.150 Water bridges: B:R.12 Salt bridges: B:R.12 SO4.13: 2 residues within 4Å: Chain B: D.79, K.106 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.79 Salt bridges: B:K.106 SO4.14: 2 residues within 4Å: Chain B: R.44, H.45 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.44, B:H.45 SO4.15: 1 residues within 4Å: Chain B: K.58 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.58, B:T.73 Salt bridges: B:K.58

2 x 560: 5-[(3R)-3-{7-[4-(aminomethyl)phenyl]-2H-1,3-benzodioxol-5-yl}but-1-yn-1-yl]-6-ethylpyrimidine-2,4-diamine(Non-covalent)

560.8: 15 residues within 4Å: Chain A: I.5, A.6, A.7, E.17, D.27, L.28, F.31, K.32, T.46, S.49, I.50, L.54, I.94, Y.100, T.113 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:L.28, A:F.31, A:F.31, A:F.31, A:T.46, A:I.50, A:I.50, A:L.54, A:I.94 Hydrogen bonds: A:I.5, A:A.6, A:A.7, A:E.17, A:K.32, A:K.32, A:Y.100, A:T.113 Water bridges: A:A.6 Salt bridges: A:D.27 560.16: 15 residues within 4Å: Chain B: I.5, A.6, A.7, E.17, D.27, L.28, F.31, K.32, T.46, S.49, I.50, L.54, I.94, Y.100, T.113 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:L.28, B:F.31, B:F.31, B:F.31, B:T.46, B:I.50, B:I.50, B:L.54, B:I.94 Hydrogen bonds: B:I.5, B:A.6, B:A.7, B:E.17, B:E.17, B:K.32, B:K.32, B:T.113 Water bridges: B:A.6, B:Y.100, B:Y.100 Salt bridges: B:D.27

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

2022-07-27

Peptides

Dihydrofolate reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Dihydrofolate reductase

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