SMTL ID : 8f5w.1 (1 other biounit)

Dihydropyrimidine Dehydrogenase (DPD) C671S Mutant Soaked with Dihydrothymine and NADPH Quasi-Anaerobically

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-dimer

Ligands

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

SF4.1: 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 SF4.2: 11 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, M.1004 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.963, A:C.986, A:C.989, A:C.992 SF4.3: 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 SF4.4: 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 SF4.9: 11 residues within 4Å: Chain B: A.946, 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 B, Metal complexes: B:C.963, B:C.986, B:C.989, B:C.992 SF4.10: 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 SF4.11: 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 SF4.12: 14 residues within 4Å: Chain B: 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 B, Metal complexes: B:C.91, B:C.130, B:C.136

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

FAD.5: 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, V.447, G.480, D.481, N.487, T.488, T.489, S.492 Ligands: NAP.6 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:L.226, 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:G.225, A:L.226, A:R.235, A:R.235, A:L.261, A:L.261, A:D.481, A:N.487, A:T.489, A:S.492, A:S.492 Water bridges: A:G.196, A:K.219, A:S.227, A:L.285, A:L.285, A:I.482, A:I.482, A:T.489, A:V.490 FAD.13: 34 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, N.487, T.488, T.489, S.492 Ligands: NAP.14 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:L.226, 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:N.487, B:T.489, B:S.492 Water bridges: B:S.199, B:S.227, B:S.227, B:G.284, B:L.285, B:L.285, B:I.482

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

NAP.6: 17 residues within 4Å: Chain A: P.131, D.291, A.340, G.341, D.342, T.343, R.364, K.365, R.371, V.373, E.376, P.393, A.437, F.438, G.439, N.487 Ligands: FAD.5 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:D.342 Hydrogen bonds: A:D.291, A:A.340, A:G.341, A:D.342, A:D.342, A:T.343, A:T.343, A:R.364, A:R.371 Water bridges: A:A.344, A:A.344 Salt bridges: A:R.364, A:K.365, A:R.371 pi-Stacking: A:F.438, A:F.438 pi-Cation interactions: A:R.364, A:R.364 NAP.14: 19 residues within 4Å: Chain B: P.131, L.285, K.289, D.291, A.340, G.341, D.342, T.343, R.364, K.365, R.371, P.393, A.437, F.438, G.439, D.481, N.487, T.488 Ligands: FAD.13 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:D.342 Hydrogen bonds: B:K.289, B:D.291, B:A.340, B:G.341, B:T.343, B:T.343, B:D.481, B:N.487 Water bridges: B:A.344, B:A.437, B:G.439 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 FNR: 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL(Non-covalent)

FNR.7: 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 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:A.551, A:A.552, A:I.590, A:N.609 Hydrogen bonds: A:S.550, A:K.574, A:K.574, A:T.575, A:T.575, A:T.575, 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:G.794 FNR.16: 25 residues within 4Å: Chain B: A.549, S.550, A.551, A.552, K.574, T.575, I.590, N.609, E.611, L.612, 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.15 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: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:G.794, B:G.794

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: FNR.7 7 PLIP interactions: 7 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 TDR.15: 9 residues within 4Å: Chain B: N.609, E.611, L.612, I.613, N.668, S.670, N.736, T.737 Ligands: FNR.16 7 PLIP interactions: 7 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Smith, M.M. et al., Mammalian dihydropyrimidine dehydrogenase: Added mechanistic details from transient-state analysis of charge transfer complexes. Arch.Biochem.Biophys. (2023)

Release Date

2023-02-01

Peptides

Dihydropyrimidine dehydrogenase [NADP(+)]: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydropyrimidine dehydrogenase [NADP(+)]

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