SMTL ID : 4eck.1

Crystal Structure of the Toxoplasma gondii TS-DHFR

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.52 Å

Oligo State

homo-dimer

Ligands

2 x UMP: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE(Covalent)

UMP.1: 15 residues within 4Å: Chain A: R.344, Y.429, C.489, H.490, Q.509, R.510, S.511, C.512, D.513, N.521, H.551, Y.553 Chain B: R.469, R.470 Ligands: CB3.2 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:D.513 Hydrogen bonds: A:Y.429, A:Q.509, A:S.511, A:D.513, A:N.521, A:N.521, A:H.551, A:Y.553 Salt bridges: A:R.344, A:R.510, B:R.469, B:R.470 UMP.5: 15 residues within 4Å: Chain A: R.469, R.470 Chain B: R.344, L.486, C.489, H.490, Q.509, R.510, S.511, C.512, D.513, N.521, H.551, Y.553 Ligands: CB3.6 10 PLIP interactions: 2 interactions with chain A, 8 interactions with chain B Salt bridges: A:R.469, A:R.470, B:R.344, B:R.510 Hydrogen bonds: B:Q.509, B:S.511, B:D.513, B:N.521, B:N.521, B:H.551

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

CB3.2: 15 residues within 4Å: Chain A: F.374, E.381, I.402, W.403, N.406, D.513, L.516, G.517, F.520, N.521, Y.553, R.603, M.608, A.609 Ligands: UMP.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.402, A:I.402, A:W.403, A:F.520, A:F.520, A:N.521 Hydrogen bonds: A:G.517, A:Y.553, A:A.609 Salt bridges: A:D.513, A:R.603, A:R.603 pi-Stacking: A:F.520 CB3.6: 16 residues within 4Å: Chain B: K.371, F.374, E.381, I.402, W.403, N.406, D.513, L.516, G.517, F.520, N.521, Y.553, R.603, M.608, A.609 Ligands: UMP.5 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.374, B:I.402, B:L.516, B:F.520 Hydrogen bonds: B:D.513, B:A.609 Salt bridges: B:K.371, B:D.513 pi-Stacking: B:W.403, B:F.520

2 x FOL: FOLIC ACID(Non-covalent)

FOL.3: 16 residues within 4Å: Chain A: V.8, V.9, A.10, L.23, D.31, F.32, F.35, S.36, M.87, F.91, L.94, V.95, R.97, V.151, T.172 Ligands: NDP.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.32, A:F.35, A:F.35, A:F.91 Hydrogen bonds: A:V.8, A:V.9, A:A.10, A:S.36, A:T.172 Salt bridges: A:D.31, A:R.97 pi-Stacking: A:F.32 FOL.7: 15 residues within 4Å: Chain B: V.8, V.9, A.10, L.23, D.31, F.32, F.35, S.36, M.87, F.91, L.94, R.97, V.151, T.172 Ligands: NDP.8 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.32, B:F.35, B:F.91 Hydrogen bonds: B:V.8, B:S.36, B:T.172, B:T.172 Salt bridges: B:D.31, B:R.97 pi-Stacking: B:F.32, B:F.35, B:F.35

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

NDP.4: 27 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, S.86, V.102, S.103, S.104, S.105, V.151, G.153, A.154, G.155, L.156, Y.157, A.159, V.182 Ligands: FOL.3 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:T.83 Hydrogen bonds: A:A.10, A:I.17, A:G.18, A:G.22, A:R.81, A:R.81, A:K.82, A:K.82, A:T.83, A:S.86, A:S.86, A:S.104, A:S.105, A:A.154, A:G.155 Salt bridges: A:R.81 NDP.8: 26 residues within 4Å: Chain B: V.8, 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, S.86, V.102, S.103, S.104, S.105, G.153, A.154, G.155, L.156, A.159, V.182 Ligands: FOL.7 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:L.23, B:T.83 Hydrogen bonds: B:I.17, B:N.21, B:N.21, B:G.80, B:R.81, B:R.81, B:K.82, B:K.82, B:K.82, B:T.83, B:S.86, B:S.103, B:S.104, B:S.105, B:G.153, B:A.154, B:G.155 Salt bridges: B:R.81, B:K.82

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

2013-10-02

Peptides

Bifunctional dihydrofolate reductase-thymidylate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Bifunctional dihydrofolate reductase-thymidylate synthase

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