SMTL ID : 1j3j.1

Double mutant (C59R+S108N) Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with pyrimethamine, NADPH, and dUMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-2-2-mer

Ligands

2 x CP6: 5-(4-CHLORO-PHENYL)-6-ETHYL-PYRIMIDINE-2,4-DIAMINE(Non-covalent)

CP6.1: 13 residues within 4Å: Chain A: I.14, C.15, A.16, D.54, M.55, F.58, N.108, S.111, I.112, I.164, Y.170, T.185 Ligands: NDP.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.58, A:I.164 Hydrogen bonds: A:I.164, A:Y.170, A:T.185, A:T.185 Salt bridges: A:D.54 pi-Stacking: A:F.58 Halogen bonds: A:N.108 CP6.3: 12 residues within 4Å: Chain B: I.14, C.15, A.16, D.54, F.58, N.108, S.111, I.112, I.164, Y.170, T.185 Ligands: NDP.4 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.58, B:F.58, B:I.164 Hydrogen bonds: B:C.15, B:Y.170, B:T.185 Salt bridges: B:D.54 Halogen bonds: B:N.108

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

NDP.2: 28 residues within 4Å: Chain A: C.15, A.16, L.40, G.41, G.44, V.45, L.46, W.48, G.105, R.106, T.107, N.108, L.127, S.128, R.129, T.130, N.144, K.145, I.164, G.165, G.166, S.167, V.168, V.169, Y.170, E.172, V.195 Ligands: CP6.1 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:L.40, A:Y.170 Hydrogen bonds: A:A.16, A:L.40, A:G.105, A:G.105, A:R.106, A:T.107, A:T.107, A:N.108, A:S.111, A:S.111, A:R.129, A:R.129, A:T.130, A:G.166, A:S.167, A:V.168, A:V.169, A:E.172 Water bridges: A:N.42, A:G.44, A:S.167, A:S.167 Salt bridges: A:R.106 pi-Cation interactions: A:R.129 NDP.4: 29 residues within 4Å: Chain B: C.15, A.16, L.40, G.41, G.44, V.45, L.46, W.48, G.105, R.106, T.107, N.108, S.111, L.127, S.128, R.129, T.130, N.144, K.145, I.164, G.165, G.166, S.167, V.168, V.169, Y.170, E.172, V.195 Ligands: CP6.3 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:L.40, B:Y.170 Hydrogen bonds: B:A.16, B:L.40, B:R.106, B:R.106, B:N.108, B:S.111, B:S.111, B:R.129, B:R.129, B:T.130, B:T.130, B:V.146, B:G.166, B:S.167, B:V.168, B:Y.170, B:E.172 Water bridges: B:G.41, B:G.44, B:T.107 Salt bridges: B:R.106

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

UMP.5: 13 residues within 4Å: Chain C: C.210, H.211, Q.229, R.230, S.231, C.232, D.233, G.237, N.241, H.271, Y.273 Chain D: R.190, R.191 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:Q.229, C:S.231, C:D.233, C:N.241, C:N.241, C:H.271 Salt bridges: C:R.230, D:R.190, D:R.191 Water bridges: D:R.190 UMP.6: 14 residues within 4Å: Chain C: R.190, R.191 Chain D: C.210, H.211, Q.229, R.230, S.231, C.232, D.233, G.237, V.238, N.241, H.271, Y.273 11 PLIP interactions: 8 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:Q.229, D:S.231, D:D.233, D:N.241, D:N.241, D:H.271, D:Y.273 Salt bridges: D:R.230, C:R.190, C:R.191 Water bridges: C:R.190

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yuvaniyama, J. et al., Insights into antifolate resistance from malarial DHFR-TS structures. NAT.STRUCT.BIOL. (2003)

Release Date

2003-05-06

Peptides

Bifunctional dihydrofolate reductase-thymidylate synthase: AB
Bifunctional dihydrofolate reductase-thymidylate synthase: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Bifunctional dihydrofolate reductase-thymidylate synthase

Bifunctional dihydrofolate reductase-thymidylate synthase

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