SMTL ID : 6ojs.1 (2 other biounits)

Crystal structure of TS-DHFR from Cryptosporidium hominis in complex with NADPH, FdUMP, MTX and 2-amino-4-oxo-4,7-dihydro-pyrrolo[2,3-d]pyrimidine-methyl-phenyl-D-glutamic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.21 Å

Oligo State

homo-dimer

Ligands

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

NDP.1: 27 residues within 4Å: Chain A: V.10, A.11, I.19, G.20, I.21, G.23, Q.24, L.25, G.55, R.56, K.57, T.58, I.75, S.76, S.77, S.78, R.92, C.113, G.114, G.115, E.116, S.117, I.118, Y.119, D.121, T.145 Ligands: MTX.4 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:L.25, A:T.58 Hydrogen bonds: A:A.11, A:I.19, A:I.21, A:G.23, A:G.23, A:R.56, A:R.56, A:K.57, A:T.58, A:T.58, A:S.76, A:S.77, A:S.78, A:G.114, A:E.116, A:S.117, A:S.117, A:I.118, A:D.121, A:D.121 Salt bridges: A:R.56 NDP.5: 27 residues within 4Å: Chain B: V.10, A.11, I.19, G.20, I.21, G.23, Q.24, L.25, G.55, R.56, K.57, T.58, I.75, S.76, S.77, S.78, R.92, C.113, G.114, G.115, E.116, S.117, I.118, Y.119, D.121, T.145 Ligands: MTX.8 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:T.58 Hydrogen bonds: B:A.11, B:I.19, B:I.21, B:G.23, B:R.56, B:K.57, B:K.57, B:T.58, B:S.61, B:S.61, B:S.76, B:S.77, B:S.78, B:G.114, B:E.116, B:S.117, B:S.117, B:I.118, B:D.121, B:T.145 Salt bridges: B:R.56, B:K.57, B:K.57

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

UFP.2: 17 residues within 4Å: Chain A: R.257, W.316, L.399, C.402, H.403, Q.422, R.423, S.424, C.425, D.426, G.430, N.434, H.464, Y.466 Chain B: R.382, R.383 Ligands: D96.3 12 PLIP interactions: 2 interactions with chain B, 10 interactions with chain A Salt bridges: B:R.382, B:R.383, A:R.257, A:R.423 Hydrophobic interactions: A:D.426 Hydrogen bonds: A:S.424, A:S.424, A:D.426, A:D.426, A:N.434, A:N.434, A:H.464 UFP.6: 18 residues within 4Å: Chain A: R.382, R.383 Chain B: R.257, W.316, Y.342, L.399, C.402, H.403, Q.422, R.423, S.424, C.425, D.426, G.430, N.434, H.464, Y.466 Ligands: D96.7 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:D.426 Hydrogen bonds: B:S.424, B:D.426, B:D.426, B:N.434, B:N.434, B:H.464, B:Y.466 Salt bridges: B:R.257, B:R.423, A:R.382, A:R.383

2 x D96: N-{4-[(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}-D-glutamic acid(Non-covalent)

D96.3: 15 residues within 4Å: Chain A: K.284, A.287, I.315, W.316, N.319, L.399, D.426, L.429, G.430, F.433, Y.466, I.515, M.519, A.520 Ligands: UFP.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.315, A:L.429, A:L.429, A:F.433, A:F.433 Hydrogen bonds: A:R.257, A:N.319, A:N.319, A:D.426, A:Y.466 Salt bridges: A:K.284, A:D.426 pi-Stacking: A:W.316 D96.7: 15 residues within 4Å: Chain B: R.257, K.284, A.287, I.315, N.319, L.399, D.426, L.429, G.430, F.433, Y.466, I.515, M.519, A.520 Ligands: UFP.6 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:I.315, B:I.315, B:L.429, B:L.429, B:F.433 Hydrogen bonds: B:R.257, B:S.290, B:N.319, B:N.319, B:D.426, B:D.426, B:Y.466, B:I.515 Salt bridges: B:K.284 pi-Stacking: B:W.316

2 x MTX: METHOTREXATE(Non-covalent)

MTX.4: 17 residues within 4Å: Chain A: V.9, V.10, A.11, L.25, D.32, L.33, K.34, F.36, S.37, T.58, I.62, L.67, R.70, C.113, Y.119, T.134 Ligands: NDP.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.33, A:F.36 Hydrogen bonds: A:V.10, A:S.37, A:C.113, A:Y.119 Salt bridges: A:D.32, A:R.70 MTX.8: 16 residues within 4Å: Chain B: V.9, V.10, A.11, L.25, D.32, L.33, F.36, S.37, T.58, I.62, L.67, R.70, C.113, Y.119, T.134 Ligands: NDP.5 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.33, B:F.36, B:L.67 Hydrogen bonds: B:V.9, B:V.10, B:S.37, B:Y.119, B:T.134 Salt bridges: B:D.32, B:K.34, B:R.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Czyzyk, D.J. et al., Understanding the structural basis of species selective, stereospecific inhibition for Cryptosporidium and human thymidylate synthase. Febs Lett. (2019)

Release Date

2019-06-19

Peptides

Bifunctional dihydrofolate reductase-thymidylate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Bifunctional dihydrofolate reductase-thymidylate synthase

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