SMTL ID : 2oip.1 (2 other biounits)

Crystal Structure of the S290G Active Site Mutant of TS-DHFR from Cryptosporidium hominis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

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

UMP.1: 15 residues within 4Å: Chain A: R.255, L.397, C.400, H.401, Q.420, R.421, S.422, C.423, D.424, N.432, H.462, Y.464 Chain B: R.380, R.381 Ligands: CB3.2 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:D.424 Hydrogen bonds: A:S.422, A:D.424, A:N.432, A:N.432, A:H.462, A:Y.464, B:R.380 Salt bridges: A:R.255, A:R.421, B:R.380, B:R.381 UMP.5: 16 residues within 4Å: Chain A: R.380, R.381 Chain B: R.255, Y.340, C.400, H.401, Q.420, R.421, S.422, C.423, D.424, G.428, N.432, H.462, Y.464 Ligands: CB3.6 10 PLIP interactions: 2 interactions with chain A, 8 interactions with chain B Salt bridges: A:R.380, A:R.381, B:R.255, B:R.421 Hydrogen bonds: B:Y.340, B:S.422, B:D.424, B:N.432, B:N.432, B:H.462

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

CB3.2: 14 residues within 4Å: Chain A: A.285, E.292, I.313, N.317, D.424, L.427, G.428, F.431, N.432, Y.464, M.515, M.517, A.518 Ligands: UMP.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.313, A:I.313, A:F.431 Hydrogen bonds: A:A.518, A:A.518, A:A.518 Water bridges: A:K.282, A:K.282, A:G.288 Salt bridges: A:K.282, A:D.424 pi-Stacking: A:F.431 CB3.6: 14 residues within 4Å: Chain B: A.285, E.292, I.313, W.314, N.317, D.424, L.427, G.428, F.431, N.432, Y.464, M.517, A.518 Ligands: UMP.5 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.313, B:I.313, B:F.431 Hydrogen bonds: B:A.518, B:A.518, B:A.518 Salt bridges: B:K.282, B:D.424 pi-Stacking: B:W.314, B:F.431

2 x MTX: METHOTREXATE(Non-covalent)

MTX.3: 17 residues within 4Å: Chain A: V.7, V.8, A.9, L.23, D.30, L.31, K.32, F.34, S.35, T.56, I.60, L.65, R.68, C.111, Y.117, T.132 Ligands: NDP.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.31, A:F.34, A:F.34, A:I.60 Hydrogen bonds: A:C.111, A:T.132, A:T.132 Water bridges: A:V.8, A:T.132 Salt bridges: A:D.30, A:R.68 pi-Stacking: A:F.34 MTX.7: 17 residues within 4Å: Chain B: V.7, V.8, A.9, L.23, D.30, L.31, K.32, F.34, S.35, T.56, I.60, L.65, R.68, C.111, Y.117, T.132 Ligands: NDP.8 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.31, B:I.60 Hydrogen bonds: B:C.111, B:T.132, B:T.132 Water bridges: B:K.32, B:K.32, B:T.132, B:T.132 Salt bridges: B:D.30, B:K.32, B:R.68 pi-Stacking: B:F.34, B:F.34

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

NDP.4: 27 residues within 4Å: Chain A: V.8, A.9, I.17, G.18, I.19, G.21, Q.22, L.23, G.53, R.54, K.55, T.56, I.73, S.74, S.75, S.76, R.90, C.111, G.112, G.113, E.114, S.115, I.116, Y.117, D.119, T.143 Ligands: MTX.3 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:I.17, A:L.23, A:T.56 Hydrogen bonds: A:A.9, A:I.17, A:I.19, A:G.21, A:G.53, A:R.54, A:K.55, A:T.56, A:S.74, A:S.75, A:S.76, A:G.112, A:E.114, A:S.115, A:S.115, A:I.116, A:Y.117, A:D.119, A:T.143, A:T.143 Water bridges: A:K.55, A:S.59 Salt bridges: A:R.54 NDP.8: 26 residues within 4Å: Chain B: V.8, A.9, I.17, G.18, G.21, Q.22, L.23, G.53, R.54, K.55, T.56, I.73, S.74, S.75, S.76, R.90, C.111, G.112, G.113, E.114, S.115, I.116, Y.117, D.119, T.143 Ligands: MTX.7 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:L.23 Hydrogen bonds: B:A.9, B:I.17, B:I.19, B:G.21, B:G.21, B:G.53, B:R.54, B:K.55, B:T.56, B:T.56, B:S.74, B:S.75, B:S.76, B:G.112, B:E.114, B:S.115, B:S.115, B:I.116, B:Y.117, B:D.119, B:T.143 Water bridges: B:T.143 Salt bridges: B:R.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Doan, L.T. et al., Nonconserved residues Ala287 and Ser290 of the Cryptosporidium hominis thymidylate synthase domain facilitate its rapid rate of catalysis. Biochemistry (2007)

Release Date

2007-07-17

Peptides

Chain A, crystal structure of Dhfr: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Chain A, crystal structure of Dhfr

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