SMTL ID : 7fgx.2 (1 other biounit)

Toxoplasma gondii dihydrofolate reductase thymidylate synthase (TgDHFR-TS) complexed with P39, NADPH and dUMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

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

NDP.1: 28 residues within 4Å: Chain A: V.9, A.10, I.17, G.18, I.19, N.21, G.22, L.23, W.25, G.80, R.81, K.82, T.83, V.102, S.103, S.104, S.105, A.128, V.151, G.152, G.153, A.154, G.155, L.156, Y.157, A.159, V.182 Ligands: 4RI.2 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:T.83 Hydrogen bonds: A:A.10, A:I.17, A:N.21, A:G.80, A:G.80, A:R.81, A:R.81, A:K.82, A:T.83, A:S.86, A:S.86, A:S.103, A:S.104, A:S.105, A:G.153, A:A.154, A:G.155, A:G.155, A:L.156 Water bridges: A:N.21, A:N.21, A:L.130, A:L.130 Salt bridges: A:R.81 NDP.4: 28 residues within 4Å: Chain B: V.9, A.10, I.17, G.18, I.19, N.21, G.22, L.23, W.25, G.80, R.81, K.82, T.83, V.102, S.103, S.104, S.105, A.128, V.151, G.152, G.153, A.154, G.155, L.156, Y.157, A.159, V.182 Ligands: 4RI.5 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:T.83 Hydrogen bonds: B:A.10, B:I.17, B:I.19, B:G.80, B:G.80, B:R.81, B:R.81, B:K.82, B:T.83, B:T.83, B:S.86, B:S.86, B:S.103, B:S.104, B:S.105, B:G.153, B:A.154, B:G.155, B:G.155, B:L.156, B:Y.157 Water bridges: B:N.21, B:N.21, B:K.82, B:A.159 Salt bridges: B:R.81

2 x 4RI: 6-hexyl-5-phenyl-pyrimidine-2,4-diamine(Non-covalent)

4RI.2: 12 residues within 4Å: Chain A: V.8, V.9, A.10, D.31, F.32, F.35, T.83, M.87, V.151, Y.157, T.172 Ligands: NDP.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.32, A:F.32, A:F.35, A:F.35, A:F.35, A:T.83 Hydrogen bonds: A:V.8, A:V.9, A:Y.157, A:T.172 Water bridges: A:V.9 Salt bridges: A:D.31 4RI.5: 13 residues within 4Å: Chain B: V.8, V.9, A.10, D.31, F.32, F.35, T.83, M.87, L.94, V.151, Y.157, T.172 Ligands: NDP.4 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.32, B:F.32, B:F.35, B:F.35, B:T.83, B:L.94 Hydrogen bonds: B:V.8, B:V.9, B:T.172 Water bridges: B:V.9 Salt bridges: B:D.31 pi-Stacking: B:F.35

2 x UMP: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE(Non-covalent)

UMP.3: 14 residues within 4Å: Chain A: R.344, C.489, H.490, Q.509, R.510, S.511, C.512, D.513, G.517, N.521, H.551, Y.553 Chain B: R.469, R.470 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.509, A:S.511, A:S.511, A:D.513, A:N.521, A:N.521, A:H.551 Water bridges: A:R.344, A:R.344, B:R.469 Salt bridges: A:R.344, A:R.510, B:R.469, B:R.470 UMP.6: 13 residues within 4Å: Chain A: R.469, R.470 Chain B: C.489, H.490, Q.509, R.510, S.511, C.512, D.513, G.517, N.521, H.551, Y.553 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:D.513 Hydrogen bonds: B:Q.509, B:S.511, B:D.513, B:N.521, B:N.521, B:H.551, B:Y.553 Salt bridges: B:R.510, A:R.469, A:R.470 Water bridges: A:R.469

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vanichtanankul, J. et al., Structural Insight into Effective Inhibitors' Binding to Toxoplasma gondii Dihydrofolate Reductase Thymidylate Synthase. Acs Chem.Biol. (2022)

Release Date

2022-06-29

Peptides

Bifunctional dihydrofolate reductase-thymidylate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Bifunctional dihydrofolate reductase-thymidylate synthase

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