- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.87 Å
- Oligo State
- homo-dimer
- Ligands
- 8 x SF4: IRON/SULFUR CLUSTER(Covalent)(Non-covalent)
- 2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)
FAD.5: 32 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, V.447, G.480, D.481, T.488, T.489, S.492
- Ligands: NAP.7
26 PLIP interactions:26 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:G.225, A:L.226, A:R.235, A:R.235, A:L.261, A:L.261, A:D.481, A:T.489, A:S.492, A:S.492
- Water bridges: A:S.199, A:K.219, A:S.227, A:G.284, A:L.285, A:D.481, A:I.482, A:T.489
FAD.13: 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, L.310, T.343, D.346, V.447, G.480, D.481, T.488, T.489, S.492
- Ligands: NAP.14
32 PLIP interactions:32 interactions with chain B- Hydrophobic interactions: B:E.230, 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:S.492, B:S.492
- Water bridges: B:S.199, B:Q.220, B:Y.222, B:Y.222, B:S.227, B:S.227, B:L.285, B:D.481, B:D.481, B:D.481, B:I.482, B:I.482, B:A.486, B:V.490
- 2 x Y3G: 5-ethynylpyrimidine-2,4(1H,3H)-dione(Non-covalent)(Covalent)
Y3G.6: 9 residues within 4Å:- Chain A: N.609, E.611, L.612, I.613, N.668, S.670, N.736, T.737
- Ligands: FNR.8
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
Y3G.16: 10 residues within 4Å:- Chain B: N.609, E.611, L.612, I.613, N.668, S.670, C.671, N.736, T.737
- Ligands: FNR.15
6 PLIP interactions:6 interactions with chain B- Hydrophobic interactions: B:I.613
- Hydrogen bonds: B:N.609, B:N.609, B:N.668, B:N.736, B:N.736
- 2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)
NAP.7: 19 residues within 4Å:- Chain A: P.131, R.235, D.291, G.339, A.340, G.341, D.342, T.343, D.346, R.364, K.365, R.371, E.376, P.393, A.437, F.438, G.439, N.487
- Ligands: FAD.5
26 PLIP interactions:26 interactions with chain A- Hydrophobic interactions: A:D.342
- Hydrogen bonds: A:D.291, A:A.340, A:G.341, A:D.342, A:T.343, A:T.343, A:R.364, A:E.376, A:N.487
- Water bridges: A:D.342, A:D.342, A:T.343, A:A.344, A:R.364, A:R.364, A:R.364, A:G.439
- Salt bridges: A:R.364, A:K.365, A:R.371, A:R.371
- pi-Stacking: A:F.438, A:F.438
- pi-Cation interactions: A:R.364, A:R.364
NAP.14: 18 residues within 4Å:- Chain B: P.131, K.289, D.291, G.339, A.340, G.341, D.342, T.343, R.364, K.365, R.371, E.376, P.393, A.437, F.438, G.439, N.487
- Ligands: FAD.13
29 PLIP interactions:29 interactions with chain B- Hydrophobic interactions: B:D.342
- Hydrogen bonds: B:K.289, B:D.291, B:A.340, B:G.341, B:D.342, B:T.343, B:T.343, B:R.364, B:R.371, B:R.371, B:E.376, B:N.487
- Water bridges: B:G.339, B:G.339, B:A.340, B:D.342, B:T.343, B:A.344, B:R.364, B:R.364, B:G.439
- Salt bridges: B:R.364, B:K.365, 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.8: 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: Y3G.6
24 PLIP interactions:24 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:E.666, A:N.668, A:K.709, A:K.709, A:K.709, A:N.736, A:G.767, A:G.795, A:C.816, A:S.817
- Water bridges: A:S.550, A:S.640, A:G.794, A:G.794
FNR.15: 25 residues within 4Å:- Chain B: A.549, S.550, A.551, A.552, K.574, T.575, I.590, N.609, E.611, E.666, 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: Y3G.16
22 PLIP interactions:22 interactions with chain B- Hydrophobic interactions: 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: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
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Forouzesh, D.C. et al., The Interaction of Porcine Dihydropyrimidine Dehydrogenase with the Chemotherapy Sensitizer: 5-Ethynyluracil. Biochemistry (2021)
- Release Date
- 2021-04-07
- Peptides
- Dihydropyrimidine dehydrogenase [NADP(+)]: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.87 Å
- Oligo State
- homo-dimer
- Ligands
- 8 x SF4: IRON/SULFUR CLUSTER(Covalent)(Non-covalent)
- 2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)
- 2 x Y3G: 5-ethynylpyrimidine-2,4(1H,3H)-dione(Non-covalent)(Covalent)
- 2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)
- 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)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Forouzesh, D.C. et al., The Interaction of Porcine Dihydropyrimidine Dehydrogenase with the Chemotherapy Sensitizer: 5-Ethynyluracil. Biochemistry (2021)
- Release Date
- 2021-04-07
- Peptides
- Dihydropyrimidine dehydrogenase [NADP(+)]: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B