SMTL ID : 7r6g.1

Crystal structure of DfrA5 dihydrofolate reductase in complex with TRIMETHOPRIM and NADPH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.61 Å

Oligo State

homo-dimer

Ligands

2 x TOP: TRIMETHOPRIM(Non-covalent)

TOP.1: 12 residues within 4Å: Chain A: M.6, A.7, A.8, E.28, Q.29, F.32, V.43, M.51, G.52, L.54, S.97, Y.103 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:M.6, A:Y.103, A:S.116, A:S.116 Salt bridges: A:E.28 pi-Stacking: A:F.32 TOP.4: 13 residues within 4Å: Chain B: M.6, A.7, A.8, E.28, Q.29, F.32, V.43, M.51, G.52, L.54, Y.59, S.97, Y.103 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:M.6, B:Y.103, B:S.116, B:S.116 Salt bridges: B:E.28 pi-Stacking: B:F.32

2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.2: 22 residues within 4Å: Chain A: C.17, G.18, G.44, R.45, K.46, T.47, V.62, T.63, R.64, S.65, P.78, S.79, I.80, G.98, G.99, G.100, E.101, I.102, E.105, G.124, D.125, V.126 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:R.45, A:K.46, A:T.47, A:T.63, A:R.64, A:R.64, A:R.64, A:S.65, A:G.100, A:E.101, A:E.101, A:I.102, A:E.105, A:D.125 Salt bridges: A:R.45 pi-Cation interactions: A:R.64, A:R.64 NDP.5: 24 residues within 4Å: Chain B: I.15, 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, E.81, G.98, G.99, G.100, E.101, I.102, E.105, V.126 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:G.18, B:H.20, B:G.44, B:R.45, B:K.46, B:K.46, B:T.47, B:T.47, B:S.50, B:R.64, B:R.64, B:R.64, B:S.65, B:I.80, B:G.100, B:E.101, B:I.102, B:E.105 Salt bridges: B:R.45, B:K.46 pi-Cation interactions: B:R.64, B:R.64

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

SO4.3: 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

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 type 5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydrofolate reductase type 5

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