SMTL ID : 3qgt.1

Crystal structure of Wild-type PfDHFR-TS COMPLEXED WITH NADPH, dUMP AND PYRIMETHAMINE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

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, S.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:I.164 Hydrogen bonds: A:Y.170, A:Y.170, A:T.185, A:T.185 Salt bridges: A:D.54 pi-Stacking: A:F.58, A:F.58 Halogen bonds: A:S.108 CP6.4: 13 residues within 4Å: Chain B: I.14, C.15, A.16, D.54, M.55, F.58, S.108, S.111, I.112, I.164, Y.170, T.185 Ligands: NDP.5 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.164, B:I.164 Hydrogen bonds: B:I.14, B:T.185, B:T.185 Salt bridges: B:D.54 pi-Stacking: B:F.58, B:F.58 Halogen bonds: B:S.108

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

NDP.2: 29 residues within 4Å: Chain A: C.15, A.16, L.40, G.41, N.42, G.44, V.45, L.46, W.48, G.105, R.106, T.107, S.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 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:L.40 Hydrogen bonds: A:A.16, A:L.40, A:N.42, A:G.44, A:G.44, A:R.106, A:T.107, A:T.107, A:S.108, A:R.129, A:R.129, A:R.129, A:T.130, A:G.165, A:S.167, A:V.168, A:V.169, A:E.172 Water bridges: A:G.41, A:S.111 Salt bridges: A:R.106 pi-Cation interactions: A:R.129 NDP.5: 29 residues within 4Å: Chain B: C.15, A.16, L.40, G.41, N.42, G.44, V.45, L.46, W.48, G.105, R.106, T.107, S.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: CP6.4 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:N.42, B:G.44, B:G.44, B:R.106, B:R.106, B:T.107, B:T.107, B:S.108, B:R.129, B:R.129, B:T.130, B:S.167, B:V.168, B:V.169, B:Y.170, B:E.172 Water bridges: B:G.105, B:S.108 Salt bridges: B:R.106

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

UMP.3: 12 residues within 4Å: Chain A: C.490, H.491, Q.509, R.510, S.511, D.513, G.517, N.521, H.551, Y.553 Chain B: R.470, R.471 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.509, A:S.511, A:D.513, A:V.518, A:N.521, A:N.521, A:H.551 Salt bridges: A:R.510, B:R.470, B:R.471 Water bridges: B:R.470 UMP.6: 14 residues within 4Å: Chain A: R.470, R.471 Chain B: C.490, H.491, Q.509, R.510, S.511, C.512, D.513, G.517, V.518, N.521, H.551, Y.553 12 PLIP interactions: 3 interactions with chain A, 9 interactions with chain B Water bridges: A:R.470 Salt bridges: A:R.470, A:R.471, B:R.510 Hydrogen bonds: B:Q.509, B:S.511, B:D.513, B:V.518, B:N.521, B:N.521, B:H.551, B:Y.553

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vanichtanankul, J. et al., Trypanosomal dihydrofolate reductase reveals natural antifolate resistance. Acs Chem.Biol. (2011)

Release Date

2011-06-29

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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