SMTL ID : 4eil.2 (3 other biounits)

Crystal Structure of the loop truncated Toxoplasma gondii TS-DHFR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

UMP.1: 16 residues within 4Å: Chain A: R.300, L.442, C.445, H.446, Q.465, R.466, S.467, C.468, D.469, G.473, N.477, H.507, Y.509 Chain B: R.425, R.426 Ligands: CB3.2 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.465, A:S.467, A:D.469, A:N.477, A:N.477, A:H.507, A:Y.509 Salt bridges: A:R.300, A:R.466, B:R.425, B:R.426 UMP.5: 16 residues within 4Å: Chain A: R.425, R.426 Chain B: R.300, L.442, C.445, H.446, Q.465, R.466, S.467, C.468, D.469, G.473, N.477, H.507, Y.509 Ligands: CB3.6 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Q.465, B:S.467, B:D.469, B:N.477, B:N.477, B:H.507 Salt bridges: B:R.300, B:R.466, A:R.425, A:R.426 Water bridges: A:R.425

2 x CB3: 10-PROPARGYL-5,8-DIDEAZAFOLIC ACID(Non-covalent)

CB3.2: 14 residues within 4Å: Chain A: F.330, I.358, W.359, N.362, D.469, L.472, G.473, F.476, N.477, Y.509, R.559, M.564, A.565 Ligands: UMP.1 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.330, A:I.358, A:I.358, A:W.359, A:L.472, A:F.476, A:F.476 Hydrogen bonds: A:D.469, A:Y.509, A:A.565, A:A.565, A:A.565 Water bridges: A:R.300, A:K.327 Salt bridges: A:K.327, A:D.469, A:R.559, A:R.559 pi-Stacking: A:F.476 CB3.6: 17 residues within 4Å: Chain B: E.337, I.358, W.359, K.361, N.362, D.469, L.472, G.473, F.476, N.477, Y.509, Q.561, M.562, E.563, M.564, A.565 Ligands: UMP.5 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:I.358, B:I.358, B:W.359, B:L.472, B:F.476, B:F.476 Hydrogen bonds: B:D.469, B:Q.561, B:M.564, B:A.565, B:A.565, B:A.565 Water bridges: B:R.300, B:K.361, B:K.361, B:K.361 Salt bridges: B:K.361, B:D.469 pi-Stacking: B:F.476

2 x FOL: FOLIC ACID(Non-covalent)

FOL.3: 15 residues within 4Å: Chain A: V.8, V.9, A.10, D.31, F.32, K.33, F.35, S.36, M.62, F.66, L.69, R.72, V.126, T.147 Ligands: NDP.4 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.35 Hydrogen bonds: A:V.8, A:S.36, A:S.36, A:Y.132, A:T.147, A:T.147 Water bridges: A:K.40, A:S.61, A:S.61, A:V.70 Salt bridges: A:D.31, A:K.40, A:R.72 pi-Stacking: A:F.32 FOL.7: 14 residues within 4Å: Chain B: V.8, V.9, A.10, D.31, F.32, K.33, F.35, S.36, M.62, F.66, R.72, V.126, T.147 Ligands: NDP.8 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.32, B:F.32, B:F.35, B:F.66 Hydrogen bonds: B:V.8, B:F.32, B:T.147, B:T.147 Water bridges: B:K.33, B:K.33, B:V.70 Salt bridges: B:D.31, B:R.72

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

NDP.4: 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.55, R.56, K.57, T.58, S.61, V.77, S.78, S.79, S.80, A.103, V.126, G.127, G.128, A.129, G.130, L.131, Y.132, V.157 Ligands: FOL.3 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:T.58 Hydrogen bonds: A:A.10, A:I.17, A:I.19, A:N.21, A:G.55, A:R.56, A:K.57, A:T.58, A:T.58, A:S.61, A:S.79, A:S.80, A:G.127, A:G.128, A:A.129, A:G.130, A:G.130 Water bridges: A:N.21, A:S.79, A:D.156 Salt bridges: A:R.56 NDP.8: 24 residues within 4Å: Chain B: V.9, A.10, I.17, G.18, I.19, N.21, G.22, L.23, W.25, G.55, R.56, K.57, T.58, S.61, V.77, S.78, S.79, S.80, A.103, G.128, A.129, Y.132, V.157 Ligands: FOL.7 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:T.58 Hydrogen bonds: B:A.10, B:I.17, B:I.19, B:N.21, B:G.55, B:G.55, B:R.56, B:R.56, B:K.57, B:T.58, B:S.61, B:S.78, B:S.79, B:A.129 Water bridges: B:S.79, B:S.79 Salt bridges: B:R.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sharma, H. et al., First Three-Dimensional Structure of Toxoplasma gondii Thymidylate Synthase-Dihydrofolate Reductase: Insights for Catalysis, Interdomain Interactions, and Substrate Channeling. Biochemistry (2013)

Release Date

2013-10-09

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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