SMTL ID : 5ecc.2 (1 other biounit)

Klebsiella pneumoniae DfrA1 complexed with NADPH and 6-ethyl-5-(3-(2-methoxy-5-(pyridin-4-yl)phenyl)prop-1-yn-1-yl)pyrimidine-2,4-diamine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-tetramer

Ligands

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

NAP.1: 31 residues within 4Å: Chain A: 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: 6DR.2, 6DR.3, CA.5 28 PLIP interactions: 28 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.47, 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:I.102, A:Y.103 Salt bridges: A:R.45, A:K.46 pi-Cation interactions: A:R.64, A:R.64 NAP.6: 33 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 Chain D: E.130 Ligands: 6DR.7, 6DR.8, CA.22 32 PLIP interactions: 29 interactions with chain B, 3 interactions with chain D 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:K.46, B:T.47, B:T.47, B:R.64, B:R.64, B:S.65, B:G.99, B:G.100, B:E.101, B:I.102, D:E.130, D:E.130 Water bridges: B:R.45, B:R.45, B:K.46, B:E.101, B:E.101, B:E.101, D:K.104 Salt bridges: B:R.45, B:K.46 pi-Cation interactions: B:R.64, B:R.64 NAP.12: 31 residues within 4Å: Chain C: 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: 6DR.13, 6DR.14, CA.16 25 PLIP interactions: 25 interactions with chain C Hydrophobic interactions: C:I.21, C:T.47 Hydrogen bonds: C:A.8, C:I.15, C:N.17, C:G.18, C:P.19, C:G.44, C:R.45, C:R.45, C:K.46, C:T.47, C:R.64, C:R.64, C:R.64, C:S.65, C:I.80, C:G.99, C:G.100, C:E.101, C:I.102 Salt bridges: C:R.45, C:K.46 pi-Cation interactions: C:R.64, C:R.64 NAP.17: 33 residues within 4Å: Chain B: E.130 Chain D: 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: CA.11, 6DR.18, 6DR.19 32 PLIP interactions: 2 interactions with chain B, 30 interactions with chain D Hydrogen bonds: B:E.130, D:A.8, D:I.15, D:N.17, D:G.18, D:P.19, D:G.44, D:R.45, D:K.46, D:T.47, D:T.63, D:R.64, D:R.64, D:S.65, D:G.99, D:G.100, D:E.101, D:E.101, D:I.102, D:Y.103 Water bridges: B:K.104, D:R.45, D:R.45, D:K.46, D:E.101, D:E.101 Hydrophobic interactions: D:I.21, D:T.47 Salt bridges: D:R.45, D:K.46 pi-Cation interactions: D:R.64, D:R.64

8 x 6DR: 6-ethyl-5-{3-[2-methoxy-5-(pyridin-4-yl)phenyl]prop-1-yn-1-yl}pyrimidine-2,4-diamine(Non-covalent)(Covalent)

6DR.2: 15 residues within 4Å: Chain A: M.6, V.7, A.8, P.19, I.21, E.28, Q.29, F.32, S.50, M.51, S.97, Y.103, S.116 Ligands: NAP.1, 6DR.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.21, A:Q.29, A:F.32, A:F.32, A:M.51, A:M.51 Hydrogen bonds: A:S.97, A:S.116, A:S.116 Water bridges: A:S.116 Salt bridges: A:E.28 6DR.3: 16 residues within 4Å: Chain A: M.6, V.7, A.8, E.28, Q.29, F.32, V.43, T.47, M.51, G.52, Y.59, S.97, Y.103, S.116 Ligands: NAP.1, 6DR.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Q.29, A:F.32, A:F.32, A:F.32, A:F.32, A:F.32, A:T.47, A:M.51 Hydrogen bonds: A:M.6, A:Q.29, A:S.116, A:S.116 Water bridges: A:S.116 Salt bridges: A:E.28 6DR.7: 17 residues within 4Å: Chain B: M.6, V.7, A.8, P.19, I.21, E.28, Q.29, F.32, K.33, S.50, M.51, L.54, S.97, Y.103, S.116 Ligands: NAP.6, 6DR.8 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.21, B:F.32, B:F.32, B:M.51, B:M.51 Hydrogen bonds: B:S.97, B:Y.103, B:S.116, B:S.116 Water bridges: B:S.116 Salt bridges: B:E.28 6DR.8: 19 residues within 4Å: Chain B: M.6, V.7, A.8, I.21, E.28, Q.29, F.32, V.43, T.47, F.48, M.51, G.52, L.54, Y.59, S.97, Y.103, S.116 Ligands: NAP.6, 6DR.7 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:I.21, B:F.32, B:F.32, B:F.32, B:F.32, B:T.47, B:M.51, B:M.51, B:L.54, B:L.54 Hydrogen bonds: B:M.6, B:Y.103, B:S.116, B:S.116 Water bridges: B:S.116 Salt bridges: B:E.28 6DR.13: 15 residues within 4Å: Chain C: M.6, V.7, A.8, P.19, I.21, E.28, Q.29, F.32, S.50, M.51, S.97, Y.103, S.116 Ligands: NAP.12, 6DR.14 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:I.21, C:Q.29, C:F.32, C:F.32, C:M.51, C:M.51 Hydrogen bonds: C:S.97, C:Y.103, C:S.116, C:S.116 Water bridges: C:S.116 Salt bridges: C:E.28 6DR.14: 16 residues within 4Å: Chain C: M.6, V.7, A.8, E.28, Q.29, F.32, V.43, T.47, M.51, G.52, Y.59, S.97, Y.103, S.116 Ligands: NAP.12, 6DR.13 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:Q.29, C:F.32, C:F.32, C:F.32, C:F.32, C:F.32, C:T.47, C:M.51 Hydrogen bonds: C:M.6, C:Q.29, C:Y.103, C:S.116, C:S.116 Water bridges: C:S.116 Salt bridges: C:E.28 6DR.18: 17 residues within 4Å: Chain D: M.6, V.7, A.8, P.19, I.21, E.28, Q.29, F.32, K.33, S.50, M.51, L.54, S.97, Y.103, S.116 Ligands: NAP.17, 6DR.19 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:I.21, D:F.32, D:F.32, D:M.51 Hydrogen bonds: D:S.97, D:S.116, D:S.116 Water bridges: D:S.116 Salt bridges: D:E.28 6DR.19: 19 residues within 4Å: Chain D: M.6, V.7, A.8, I.21, E.28, Q.29, F.32, V.43, T.47, F.48, M.51, G.52, L.54, Y.59, S.97, Y.103, S.116 Ligands: NAP.17, 6DR.18 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:I.21, D:F.32, D:F.32, D:F.32, D:F.32, D:T.47, D:M.51, D:L.54, D:L.54 Hydrogen bonds: D:M.6, D:S.116, D:S.116 Water bridges: D:S.116 Salt bridges: D:E.28

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: K.88, K.89, I.90, T.91, D.92 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.88 Water bridges: A:D.92 GOL.9: 3 residues within 4Å: Chain B: D.125 Chain D: K.46 Ligands: GOL.20 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.125 Water bridges: B:K.46, B:E.101, B:Y.127 GOL.15: 5 residues within 4Å: Chain C: K.88, K.89, I.90, T.91, D.92 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.88 GOL.20: 3 residues within 4Å: Chain B: K.46 Chain D: D.125 Ligands: GOL.9 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:D.125 Water bridges: D:K.46, D:Y.127, B:E.101, B:E.101

6 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain A: S.79, I.80, K.81 Ligands: NAP.1 No protein-ligand interaction detected (PLIP) CA.10: 5 residues within 4Å: Chain B: E.101, K.104 Chain D: E.101, K.104 Ligands: CA.21 No protein-ligand interaction detected (PLIP) CA.11: 5 residues within 4Å: Chain B: K.104, P.129, E.130 Chain D: S.105 Ligands: NAP.17 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.105 CA.16: 4 residues within 4Å: Chain C: S.79, I.80, K.81 Ligands: NAP.12 No protein-ligand interaction detected (PLIP) CA.21: 5 residues within 4Å: Chain B: E.101, K.104 Chain D: E.101, K.104 Ligands: CA.10 No protein-ligand interaction detected (PLIP) CA.22: 5 residues within 4Å: Chain B: S.105 Chain D: K.104, P.129, E.130 Ligands: NAP.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.105

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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Dehydrofolate reductase type I

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