SMTL ID : 7rgj.1

DfrA1 complexed with NADPH and 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 1.44 Å

Oligo State

homo-dimer

Ligands

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 30 residues within 4Å: Chain A: V.7, A.8, I.15, G.16, N.17, G.18, P.19, D.20, I.21, W.23, G.44, R.45, K.46, T.47, V.62, T.63, R.64, S.65, P.78, S.79, I.80, S.97, G.98, G.99, G.100, E.101, I.102, Y.103 Ligands: CA.2, 8MU.3 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:I.21, A:T.47 Hydrogen bonds: A:A.8, A:I.15, A:N.17, A:G.18, A:P.19, A:G.44, A:R.45, A:R.45, A:K.46, A:K.46, A:T.47, A:T.63, A:R.64, A:R.64, A:S.65, A:I.80, A:G.99, A:G.100, A:E.101, A:E.101, A:I.102, A:Y.103 Water bridges: A:R.64 Salt bridges: A:R.45, A:K.46 pi-Cation interactions: A:R.64, A:R.64 NAP.4: 30 residues within 4Å: Chain B: V.7, A.8, I.15, G.16, N.17, G.18, P.19, D.20, I.21, G.44, R.45, K.46, T.47, V.62, T.63, R.64, S.65, P.78, S.79, I.80, S.97, G.98, G.99, G.100, E.101, I.102, Y.103, V.126 Ligands: CA.5, 560.6 32 PLIP interactions: 32 interactions with chain B Hydrophobic interactions: B:I.21, B:T.47 Hydrogen bonds: B:A.8, B:N.17, B:G.18, B:P.19, B:G.44, B:R.45, B:R.45, B:K.46, B:T.47, B:R.64, B:R.64, B:R.64, B:S.65, B:I.80, B:G.99, B:G.100, B:E.101, B:I.102, B:Y.103 Water bridges: B:K.46, B:S.50, B:R.64, B:E.101, B:E.101, B:E.101, B:S.105 Salt bridges: B:R.45, B:K.46 pi-Cation interactions: B:R.64, B:R.64

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 2 residues within 4Å: Chain A: S.105 Ligands: NAP.1 No protein-ligand interaction detected (PLIP) CA.5: 4 residues within 4Å: Chain B: S.79, I.80, K.81 Ligands: NAP.4 No protein-ligand interaction detected (PLIP)

2 x 8MU: 5-[(3S)-3-{7-[4-(aminomethyl)phenyl]-2H-1,3-benzodioxol-5-yl}but-1-yn-1-yl]-6-ethylpyrimidine-2,4-diamine(Non-covalent)

8MU.3: 13 residues within 4Å: Chain A: M.6, V.7, A.8, I.21, W.23, E.28, F.32, T.47, M.51, L.54, Y.103, S.116 Ligands: NAP.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.32, A:T.47, A:M.51 Hydrogen bonds: A:M.6, A:I.21, A:S.116, A:S.116 Water bridges: A:I.21 Salt bridges: A:E.28 8MU.7: 9 residues within 4Å: Chain B: W.40, K.58, E.72, N.73, L.75, I.76, F.77, N.86, I.90 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.75, B:L.75, B:F.77, B:I.90, B:I.90 Hydrogen bonds: B:E.72, B:N.73 pi-Stacking: B:W.40

1 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)

560.6: 16 residues within 4Å: Chain B: M.6, V.7, A.8, I.21, E.28, Q.29, F.32, K.33, T.47, S.50, M.51, L.54, S.97, Y.103, S.116 Ligands: NAP.4 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:I.21, B:F.32, B:F.32, B:T.47, B:M.51, B:L.54 Hydrogen bonds: B:M.6, B:Y.103, B:S.116, B:S.116 Water bridges: B:V.7, B:S.50 Salt bridges: B:E.28

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

2022-05-25

Peptides

Dihydrofolate reductase type 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydrofolate reductase type 1

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