SMTL ID : 5ecx.1

Klebsiella pneumoniae DfrA1 complexed with NADPH and 6-ethyl-5-(3-(6-(pyridin-4-yl)benzo[d][1,3]dioxol-4-yl)but-1-yn-1-yl)pyrimidine-2,4-diamine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

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

NAP.1: 29 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: 5N1.2 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: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.99, A:G.100, A:E.101, A:E.101, A:I.102, A:Y.103 Salt bridges: A:R.45, A:K.46 pi-Cation interactions: A:R.64, A:R.64 NAP.3: 30 residues within 4Å: Chain B: 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, V.126 Ligands: 5N1.4 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:I.21, B:T.47 Hydrogen bonds: B:A.8, B:I.15, 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:T.47, B:T.63, B:R.64, B:R.64, B:S.65, B:G.99, B:G.100, B:E.101, B:I.102 Water bridges: B:K.46, B:R.64, B:E.101 Salt bridges: B:R.45 pi-Cation interactions: B:R.64, B:R.64

2 x 5N1: 6-ethyl-5-[(3~{S})-3-(6-pyridin-4-yl-1,3-benzodioxol-4-yl)but-1-ynyl]pyrimidine-2,4-diamine(Non-covalent)

5N1.2: 15 residues within 4Å: Chain A: M.6, V.7, A.8, P.19, I.21, E.28, Q.29, F.32, T.47, S.50, M.51, L.54, Y.103, S.116 Ligands: NAP.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Q.29, A:F.32, A:F.32, A:F.32, A:F.32, A:T.47, A:M.51 Hydrogen bonds: A:Y.103, A:S.116, A:S.116 Water bridges: A:I.21, A:S.116 Salt bridges: A:E.28 5N1.4: 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, Y.103, S.116 Ligands: NAP.3, GOL.5 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:Q.29, B:F.32, B:F.32, B:F.32, B:F.32, B:T.47, B:M.51, B:L.54 Hydrogen bonds: B:K.33, B:S.97, B:Y.103, B:S.116, B:S.116 Water bridges: B:S.116 Salt bridges: B:E.28

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain B: W.23, S.24, Q.29 Ligands: 5N1.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.29 Water bridges: B:W.23, B:A.25

1 x GLV: GLYOXYLIC ACID(Non-covalent)

GLV.6: 8 residues within 4Å: Chain A: D.142, F.143, A.144 Chain B: N.38, Q.39, W.40, K.58, T.91 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.91, A:A.144 Water bridges: B:W.40 Salt bridges: B:K.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lombardo, M.N. et al., Crystal Structures of Trimethoprim-Resistant DfrA1 Rationalize Potent Inhibition by Propargyl-Linked Antifolates. ACS Infect Dis (2016)

Release Date

2016-05-18

Peptides

Dehydrofolate reductase type I: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dehydrofolate reductase type I

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