SMTL ID : 3dl5.2 (2 other biounits)

Crystal Structure of the A287F Active Site Mutant of TS-DHFR from Cryptosporidium hominis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.74 Å

Oligo State

homo-dimer

Ligands

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

UMP.1: 16 residues within 4Å: Chain A: R.257, Y.342, P.400, C.402, H.403, Q.422, R.423, S.424, C.425, D.426, N.434, H.464, Y.466 Chain B: R.382, R.383 Ligands: CB3.2 12 PLIP interactions: 3 interactions with chain B, 9 interactions with chain A Water bridges: B:R.383 Salt bridges: B:R.382, B:R.383, A:R.257, A:R.423 Hydrogen bonds: A:Q.422, A:S.424, A:D.426, A:N.434, A:N.434, A:H.464, A:Y.466 UMP.5: 16 residues within 4Å: Chain A: R.382, R.383 Chain B: R.257, Y.342, P.400, C.402, H.403, Q.422, R.423, S.424, C.425, D.426, N.434, H.464, Y.466 Ligands: CB3.6 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.422, B:S.424, B:S.424, B:D.426, B:N.434, B:N.434, B:H.464 Salt bridges: B:R.257, B:R.423, A:R.382, A:R.383

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

CB3.2: 15 residues within 4Å: Chain A: F.287, S.290, E.294, I.315, N.319, L.399, D.426, L.429, G.430, F.433, N.434, Y.466, M.519, A.520 Ligands: UMP.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.315, A:I.315, A:L.399, A:F.433 Hydrogen bonds: A:S.290, A:Y.466, A:A.520, A:A.520, A:A.520 Water bridges: A:K.284, A:S.290 Salt bridges: A:K.284, A:D.426 pi-Stacking: A:F.433 CB3.6: 16 residues within 4Å: Chain B: F.287, S.290, E.294, I.315, W.316, N.319, L.399, D.426, L.429, G.430, F.433, N.434, Y.466, M.519, A.520 Ligands: UMP.5 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:I.315, B:I.315, B:L.399, B:F.433, B:F.433, B:F.433 Hydrogen bonds: B:S.290, B:A.520, B:A.520, B:A.520 Water bridges: B:K.284 Salt bridges: B:K.284, B:D.426 pi-Stacking: B:W.316

2 x DHF: DIHYDROFOLIC ACID(Non-covalent)

DHF.3: 15 residues within 4Å: Chain A: V.9, V.10, A.11, L.25, D.32, L.33, K.34, F.36, S.37, I.62, L.67, R.70, C.113, T.134 Ligands: NDP.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.33, A:L.33, A:I.62 Hydrogen bonds: A:T.134, A:T.134 Water bridges: A:T.134 Salt bridges: A:D.32, A:R.70 pi-Stacking: A:F.36, A:F.36 DHF.7: 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.8 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:L.33, B:L.33, B:I.62 Hydrogen bonds: B:V.9, B:S.37, B:Y.119, B:T.134, B:T.134 Water bridges: B:V.10, B:D.32, B:D.32 Salt bridges: B:D.32, B:K.34, B:R.70 pi-Stacking: B:F.36, B:F.36

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

NDP.4: 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: DHF.3 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:L.25 Hydrogen bonds: A:A.11, A:I.19, A:I.21, A:G.23, A:G.23, A:G.55, A:R.56, A:K.57, A:T.58, A:S.77, A:S.78, A:G.114, A:E.116, A:S.117, A:S.117, A:I.118, A:Y.119, A:D.121, A:T.145, A:T.145 Water bridges: A:K.57 Salt bridges: A:R.56 NDP.8: 26 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, T.145 Ligands: DHF.7 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:T.58 Hydrogen bonds: B:A.11, B:I.19, B:I.21, B:G.23, B:G.23, B:G.55, B:R.56, B:K.57, B:T.58, B:T.58, 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:Y.119 Water bridges: B:K.57, B:T.145, B:T.145 Salt bridges: B:R.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martucci, W.E. et al., Explaining an unusually fast parasitic enzyme: folate tail-binding residues dictate substrate positioning and catalysis in Cryptosporidium hominis thymidylate synthase. Biochemistry (2008)

Release Date

2008-08-19

Peptides

Dihydrofolate reductase, DHFR: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydrofolate reductase, DHFR

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