SMTL ID : 7mqp.1

E. coli dihydrofolate reductase complexed with 4'-chloro-3'-(4-(2,4-diamino-6-ethylpyrimidin-5-yl)but-3-yn-2-yl)-[1,1'-biphenyl]-4-carboxamide (UCP1228)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x ZM4: 3'-[(2S)-4-(2,4-diamino-6-ethylpyrimidin-5-yl)but-3-yn-2-yl]-4'-methyl[1,1'-biphenyl]-4-carboxamide(Non-covalent)

ZM4.1: 17 residues within 4Å: Chain A: I.5, A.6, A.7, M.16, E.17, N.18, D.27, L.28, F.31, K.32, T.46, S.49, I.50, L.54, I.94, Y.100, T.113 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:E.17, A:L.28, A:F.31, A:F.31, A:F.31, A:T.46, A:I.50, A:L.54, A:I.94 Hydrogen bonds: A:I.5, A:A.7, A:Y.100, A:T.113, A:T.113 Water bridges: A:A.6 Salt bridges: A:E.17, A:D.27 ZM4.9: 17 residues within 4Å: Chain B: I.5, A.6, A.7, M.16, E.17, N.18, D.27, L.28, F.31, K.32, T.46, S.49, I.50, L.54, I.94, Y.100, T.113 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:E.17, B:L.28, B:F.31, B:F.31, B:F.31, B:T.46, B:I.50, B:L.54, B:I.94 Hydrogen bonds: B:I.5, B:A.7, B:T.113, B:T.113 Water bridges: B:A.6 Salt bridges: B:E.17, B:D.27

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

SO4.2: 8 residues within 4Å: Chain A: G.43, R.44, H.45, T.46, G.95, G.96, R.98, V.99 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.43, A:G.43, A:H.45, A:T.46, A:T.46, A:G.96 Water bridges: A:R.44, A:R.98, A:R.98 Salt bridges: A:H.45, A:R.98 SO4.3: 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 Water bridges: A:R.44, A:R.44 Salt bridges: A:R.44, A:R.98 SO4.4: 6 residues within 4Å: Chain A: L.104, Y.128, E.129, D.132, W.133, R.158 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.129, A:D.132, A:W.133 Salt bridges: A:R.158 SO4.5: 5 residues within 4Å: Chain A: D.116, A.143, H.149, S.150 Chain B: R.12 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.116, A:D.116, A:H.149, A:S.150, A:S.150 Water bridges: A:A.143, A:A.143 Salt bridges: B:R.12 SO4.6: 2 residues within 4Å: Chain A: R.44, H.45 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.44, A:H.45 Salt bridges: A:R.44, A:H.45 SO4.7: 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 SO4.8: 1 residues within 4Å: Chain A: K.76 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.76 SO4.10: 8 residues within 4Å: Chain B: G.43, R.44, H.45, T.46, G.95, G.96, R.98, V.99 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.43, B:G.43, B:H.45, B:T.46, B:G.96 Water bridges: B:R.44, B:R.98, B:R.98 Salt bridges: B:H.45, B:R.98 SO4.11: 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 Water bridges: B:R.44, B:R.44 Salt bridges: B:R.44, B:R.98 SO4.12: 6 residues within 4Å: Chain B: L.104, Y.128, E.129, D.132, W.133, R.158 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.129, B:W.133 Salt bridges: B:R.158 SO4.13: 5 residues within 4Å: Chain A: R.12 Chain B: D.116, A.143, H.149, S.150 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.116, B:S.150, B:S.150 Water bridges: B:A.143, B:A.143 Salt bridges: A:R.12 SO4.14: 2 residues within 4Å: Chain B: R.44, H.45 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.44, B:H.45 Salt bridges: B:R.44, B:H.45 SO4.15: 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 SO4.16: 1 residues within 4Å: Chain B: K.76 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.76

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

2022-05-11

Peptides

Dihydrofolate reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Dihydrofolate reductase

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