SMTL ID : 7m31.2 (1 other biounit)

Dihydropyrimidine Dehydrogenase (DPD) C671S Mutant Soaked with Thymine and NADPH Anaerobically

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-dimer

Ligands

1 x PRO: PROLINE(Non-covalent)

PRO.1: 3 residues within 4Å: Chain A: P.3, G.1016, L.1017 2 PLIP interactions: 2 interactions with chain A, Hydrophobic interactions: A:P.3 Hydrogen bonds: A:L.1017

8 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.2: 13 residues within 4Å: Chain A: I.948, C.953, I.954, N.955, C.956, G.957, K.958, C.959, P.980, C.996, P.997, C.1001, I.1002 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.953, A:C.956, A:C.959, A:C.996 SF4.3: 10 residues within 4Å: Chain A: C.963, Y.968, I.971, V.982, C.986, T.987, G.988, C.989, T.990, C.992 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.963, A:C.986, A:C.989, A:C.992 SF4.4: 11 residues within 4Å: Chain A: C.79, L.80, K.81, C.82, P.86, C.87, C.140, N.141, L.142, I.150, I.152 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.79, A:C.82, A:C.87, A:C.140 SF4.5: 14 residues within 4Å: Chain A: C.91, P.92, T.93, L.95, I.97, N.120, C.126, C.130, T.132, L.135, C.136, I.152, Q.156, V.490 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.91, A:C.130, A:C.136 SF4.10: 11 residues within 4Å: Chain B: C.963, Y.968, I.971, V.982, C.986, T.987, G.988, C.989, T.990, C.992, M.1004 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.963, B:C.986, B:C.989, B:C.992 SF4.11: 13 residues within 4Å: Chain B: I.948, C.953, I.954, N.955, C.956, G.957, K.958, C.959, P.980, C.996, P.997, C.1001, I.1002 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.953, B:C.956, B:C.959, B:C.996 SF4.12: 11 residues within 4Å: Chain B: C.79, L.80, K.81, C.82, P.86, C.87, C.140, N.141, L.142, I.150, I.152 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.79, B:C.82, B:C.87, B:C.140 SF4.13: 13 residues within 4Å: Chain B: C.91, P.92, T.93, L.95, I.97, N.120, C.130, T.132, L.135, C.136, I.152, Q.156, V.490 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.91, B:C.130, B:C.136

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.6: 33 residues within 4Å: Chain A: V.129, P.131, G.194, A.195, G.196, P.197, A.198, E.218, K.219, Q.220, G.225, L.226, E.230, I.231, R.235, K.259, S.260, L.261, G.282, I.283, G.284, P.286, L.310, T.343, D.346, E.376, V.447, G.480, D.481, T.488, T.489, S.492 Ligands: NAP.7 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:E.230, A:I.231, A:L.310, A:T.343 Hydrogen bonds: A:V.129, A:A.195, A:A.198, A:K.219, A:K.219, A:G.225, A:L.226, A:R.235, A:R.235, A:L.261, A:L.261, A:E.376, A:D.481, A:T.489, A:T.489, A:S.492, A:S.492 Water bridges: A:G.196, A:Y.222, A:S.227, A:G.284, A:L.285, A:L.285, A:D.481, A:D.481, A:I.482, A:A.486, A:T.489, A:V.490 FAD.14: 32 residues within 4Å: Chain B: V.129, P.131, G.194, A.195, G.196, P.197, A.198, F.217, E.218, K.219, Q.220, G.225, L.226, E.230, I.231, R.235, K.259, S.260, L.261, G.282, I.283, G.284, P.286, L.310, T.343, D.346, V.447, G.480, D.481, T.488, T.489, S.492 29 PLIP interactions: 29 interactions with chain B Hydrophobic interactions: B:I.231, B:L.310, B:T.343 Hydrogen bonds: B:V.129, B:A.195, B:A.198, B:K.219, B:G.225, B:L.226, B:R.235, B:R.235, B:L.261, B:L.261, B:D.481, B:T.489, B:T.489, B:S.492 Water bridges: B:S.199, B:Q.220, B:Y.222, B:S.227, B:G.284, B:L.285, B:L.285, B:D.481, B:I.482, B:A.486, B:T.489, B:V.490

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.7: 17 residues within 4Å: Chain A: P.131, K.289, D.291, G.339, A.340, G.341, D.342, T.343, R.364, K.365, E.376, P.393, A.437, F.438, G.439, N.487 Ligands: FAD.6 31 PLIP interactions: 30 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:D.342 Hydrogen bonds: A:D.291, A:D.291, A:A.340, A:G.341, A:T.343, A:T.343, A:R.364, A:E.376, A:E.376 Water bridges: A:K.289, A:D.342, A:D.342, A:D.342, A:D.342, A:T.343, A:A.344, A:R.364, A:R.364, A:R.364, A:N.369, A:G.439, A:A.486, A:N.487, B:K.47 Salt bridges: A:R.364, A:K.365 pi-Stacking: A:F.438, A:F.438 pi-Cation interactions: A:R.364, A:R.364 NAP.15: 15 residues within 4Å: Chain B: K.289, D.291, G.339, A.340, G.341, D.342, T.343, R.364, K.365, R.371, P.393, A.437, F.438, G.439, N.487 28 PLIP interactions: 28 interactions with chain B Hydrogen bonds: B:D.291, B:D.291, B:A.340, B:G.341, B:D.342, B:T.343, B:T.343, B:R.364 Water bridges: B:G.341, B:D.342, B:D.342, B:R.364, B:R.364, B:R.364, B:A.437, B:G.439, B:S.440, B:S.440, B:D.481, B:A.486 Salt bridges: B:R.364, B:K.365, B:R.371, B:R.371 pi-Stacking: B:F.438, B:F.438 pi-Cation interactions: B:R.364, B:R.364

2 x TDR: THYMINE(Non-covalent)

TDR.8: 9 residues within 4Å: Chain A: N.609, E.611, L.612, I.613, N.668, S.670, N.736, T.737 Ligands: FMN.9 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.613 Hydrogen bonds: A:N.609, A:N.609, A:N.668, A:S.670, A:N.736, A:N.736, A:T.737 Water bridges: A:G.764 TDR.16: 9 residues within 4Å: Chain B: N.609, E.611, L.612, I.613, N.668, S.670, N.736, T.737 Ligands: FMN.17 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.613 Hydrogen bonds: B:N.609, B:N.609, B:N.668, B:S.670, B:N.736, B:N.736, B:T.737

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.9: 24 residues within 4Å: Chain A: A.549, S.550, A.551, A.552, K.574, T.575, I.590, N.609, E.611, N.668, K.709, T.735, N.736, T.737, S.766, G.767, T.793, G.794, G.795, V.815, C.816, S.817, Q.820 Ligands: TDR.8 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:A.552, A:I.590 Hydrogen bonds: A:S.550, A:T.575, A:T.575, A:T.575, A:E.666, A:N.668, A:K.709, A:K.709, A:N.736, A:G.767, A:T.793, A:G.795, A:C.816, A:S.817 Water bridges: A:S.550, A:G.794, A:I.796 FMN.17: 24 residues within 4Å: Chain B: A.549, S.550, A.551, A.552, K.574, T.575, I.590, N.609, E.611, N.668, K.709, T.735, N.736, T.737, S.766, G.767, T.793, G.794, G.795, V.815, C.816, S.817, Q.820 Ligands: TDR.16 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:A.551, B:A.552, B:I.590, B:N.609 Hydrogen bonds: B:S.550, B:K.574, B:T.575, B:T.575, B:T.575, B:N.668, B:K.709, B:K.709, B:N.736, B:G.767, B:T.793, B:G.795, B:C.816, B:S.817 Water bridges: B:S.550, B:S.640, B:G.794, B:I.796

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Beaupre, B.A. et al., Perturbing the Movement of Hydrogens to Delineate and Assign Events in the Reductive Activation and Turnover of Porcine Dihydropyrimidine Dehydrogenase. Biochemistry (2021)

Release Date

2021-06-09

Peptides

Dihydropyrimidine dehydrogenase [NADP(+)]: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Dihydropyrimidine dehydrogenase [NADP(+)]

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