SMTL ID : 7rgk.1

DfrA5 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 Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

homo-dimer

Ligands

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

NAP.1: 30 residues within 4Å: Chain A: A.7, A.8, I.15, G.16, C.17, G.18, P.19, H.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, E.105 Ligands: 560.4 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:T.47 Hydrogen bonds: A:A.8, A:C.17, A:G.18, A:P.19, A:G.44, A:R.45, A:K.46, A:T.47, A:T.63, A:T.63, A:R.64, A:R.64, A:R.64, A:S.65, A:I.80, A:G.98, A:G.100, A:E.101, A:E.101, A:I.102, A:Y.103, A:Y.103, A:E.105 Salt bridges: A:R.45 pi-Cation interactions: A:R.64, A:R.64 NAP.5: 30 residues within 4Å: Chain B: A.7, A.8, I.15, G.16, C.17, G.18, P.19, H.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, E.105 Ligands: SO4.6, 560.8 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:I.21, B:T.47 Hydrogen bonds: B:A.8, B:C.17, B:G.18, B:P.19, B:R.45, B:K.46, B:T.47, B:T.47, B:R.64, B:R.64, B:S.65, B:I.80, B:G.98, B:G.100, B:E.101, B:E.101, B:I.102, B:Y.103, B:E.105 Water bridges: B:S.50, B:R.64, B:R.64 Salt bridges: B:R.45, B:K.46 pi-Cation interactions: B:R.64, B:R.64

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

SO4.2: 2 residues within 4Å: Chain A: R.45, K.46 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.45, A:K.46 SO4.3: 7 residues within 4Å: Chain A: K.2, S.4, H.93 Chain B: F.139, E.140, Q.141, H.142 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:E.140, B:H.142, A:S.4, A:S.4 Water bridges: A:K.2 Salt bridges: A:K.2, A:H.93 SO4.6: 4 residues within 4Å: Chain B: S.79, I.80, E.81 Ligands: NAP.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.80, B:E.81 SO4.7: 3 residues within 4Å: Chain B: Q.29, K.33 Ligands: 560.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.29, B:Q.29 Salt bridges: B:K.33

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)

560.4: 14 residues within 4Å: Chain A: M.6, A.7, A.8, E.28, Q.29, F.32, T.47, S.50, M.51, L.54, S.97, Y.103, S.116 Ligands: NAP.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.32, A:F.32, A:T.47, A:M.51 Hydrogen bonds: A:M.6, A:S.116, A:S.116 Salt bridges: A:E.28 pi-Stacking: A:F.32 560.8: 15 residues within 4Å: Chain B: M.6, A.7, A.8, I.21, E.28, Q.29, F.32, T.47, S.50, M.51, S.97, Y.103, S.116 Ligands: NAP.5, SO4.7 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.21, B:Q.29, B:F.32, B:T.47 Hydrogen bonds: B:M.6, B:Y.103, B:S.116, B:S.116 Water bridges: B:S.116 Salt bridges: B:E.28 pi-Stacking: B:F.32

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 5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydrofolate reductase type 5

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