SMTL ID : 8f61.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

homo-dimer

Ligands

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

SF4.1: 13 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, Q.156, V.490 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.91, A:C.130, A:C.136 SF4.2: 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 SF4.3: 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 SF4.4: 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 SF4.8: 10 residues within 4Å: Chain B: C.79, L.80, K.81, C.82, 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 SF4.9: 13 residues within 4Å: Chain B: C.91, P.92, 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 SF4.10: 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 SF4.11: 11 residues within 4Å: Chain B: I.948, C.953, I.954, C.956, G.957, 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

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, F.217, E.218, K.219, Q.220, G.225, L.226, E.230, I.231, R.235, 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, N.487, T.488, T.489, S.492 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:L.226, A:L.226, 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:T.489, A:S.492, A:S.492 FAD.12: 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, 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 24 PLIP interactions: 24 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:Q.220, 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:N.487, B:T.489, B:S.492, B:S.492 Water bridges: B:G.284, B:L.285, B:V.490

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.6: 23 residues within 4Å: Chain A: A.549, S.550, A.551, A.552, K.574, T.575, I.590, N.609, L.612, N.668, K.709, T.735, N.736, T.737, S.766, G.767, T.793, G.794, G.795, C.816, S.817, Q.820 Ligands: XH5.7 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.590, A:N.609 Hydrogen bonds: A:S.550, A:S.550, A:T.575, A:T.575, A:T.575, A:N.668, A:K.709, A:N.736, A:N.736, A:S.766, A:G.767, A:T.793, A:G.795, A:C.816, A:S.817 Water bridges: A:A.818

1 x XH5: (5S)-5-methyl-1,3-diazinane-2,4-dione(Non-covalent)

XH5.7: 8 residues within 4Å: Chain A: N.609, E.611, L.612, N.668, S.670, N.736, T.737 Ligands: FMN.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.609, A:N.668, A:S.670, A:N.736, A:N.736

1 x TDR: THYMINE(Non-covalent)

TDR.13: 9 residues within 4Å: Chain B: N.609, E.611, L.612, I.613, N.668, S.670, N.736, T.737 Ligands: FNR.14 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.613 Hydrogen bonds: B:N.609, B:N.668, B:S.670, B:N.736, B:N.736

1 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.14: 23 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, C.816, S.817, Q.820 Ligands: TDR.13 20 PLIP interactions: 20 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:K.709, B:K.709, B:K.709, B:N.736, B:G.767, B:G.795, B:C.816, B:S.817 Water bridges: B:G.794, B:I.796, B:A.818

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
C

B
D

Dihydropyrimidine dehydrogenase [NADP(+)]

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