SMTL ID : 3iro.1 (1 other biounit)

Trypanosoma cruzi Dihydrofolate Reductase-Thymidylate Synthase complexed with NADPH and Q-8 antifolate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x 2CY: 5-[3-(3-fluorophenoxy)propoxy]quinazoline-2,4-diamine(Non-covalent)

2CY.1: 14 residues within 4Å: Chain A: V.26, V.27, A.28, D.48, M.49, F.52, T.80, S.83, I.84, P.85, I.154, Y.160, T.178 Ligands: NDP.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.52, A:T.80, A:I.154 Hydrogen bonds: A:V.26, A:V.27, A:Y.160 Salt bridges: A:D.48 pi-Stacking: A:F.52 2CY.7: 15 residues within 4Å: Chain B: V.26, V.27, A.28, I.41, D.48, M.49, F.52, R.53, T.80, I.84, P.85, L.91, I.154, T.178 Ligands: NDP.8 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.41, B:T.80, B:L.91 Hydrogen bonds: B:V.26, B:Y.160, B:T.178, B:T.178 Salt bridges: B:D.48 pi-Stacking: B:F.52

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

NDP.2: 27 residues within 4Å: Chain A: V.27, A.28, I.35, G.38, R.39, S.40, I.41, W.43, G.77, R.78, K.79, T.80, S.83, L.99, S.100, S.101, T.102, G.130, G.131, I.154, G.155, G.156, G.157, S.158, V.159, Y.160 Ligands: 2CY.1 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.41 Hydrogen bonds: A:A.28, A:I.35, A:G.77, A:G.77, A:R.78, A:K.79, A:T.80, A:S.83, A:S.83, A:S.100, A:S.101, A:T.102, A:G.157, A:S.158, A:S.158, A:V.159 Salt bridges: A:R.78 NDP.8: 25 residues within 4Å: Chain B: A.28, I.35, G.38, R.39, S.40, I.41, G.77, R.78, K.79, T.80, S.83, L.99, S.100, S.101, T.102, G.130, G.131, I.154, G.155, G.156, G.157, S.158, V.159, Y.160 Ligands: 2CY.7 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:I.41 Hydrogen bonds: B:A.28, B:I.35, B:G.38, B:S.40, B:G.77, B:R.78, B:K.79, B:T.80, B:T.80, B:S.83, B:S.83, B:S.101, B:S.101, B:T.102, B:G.157, B:S.158, B:S.158, B:V.159 Salt bridges: B:R.78

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 4 residues within 4Å: Chain A: R.383, R.384 Chain B: R.423, S.424 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Salt bridges: A:R.383, A:R.384, B:R.423 Hydrogen bonds: B:S.424 PO4.9: 4 residues within 4Å: Chain A: R.423, S.424 Chain B: R.383, R.384 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.383, A:S.424, A:S.424 Salt bridges: B:R.384, A:R.423

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 3 residues within 4Å: Chain A: V.193, W.206, R.208 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.193 Salt bridges: A:R.208 ACT.5: 4 residues within 4Å: Chain A: V.253, H.255, L.263, S.467 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.253, A:L.263 Hydrogen bonds: A:S.467 Salt bridges: A:H.255 ACT.6: 2 residues within 4Å: Chain A: I.248, N.474 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.248 Hydrogen bonds: A:N.474 ACT.11: 7 residues within 4Å: Chain B: C.403, Q.422, S.424, C.425, D.426, G.430, N.434 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.422, B:D.426

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 6 residues within 4Å: Chain A: W.390 Chain B: A.371, I.372, T.375, D.382, R.384 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:W.390, B:L.386 Hydrogen bonds: B:D.382

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chitnumsub, P. et al., Structural basis of antifolate inhibition of Trypanosoma cruzi Dihydrofolate Reductase-Thymidylate Synthase. To be Published

Release Date

2010-07-28

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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