SMTL ID : 7m32.2 (1 other biounit)

Dihydropyrimidine Dehydrogenase (DPD) C671A Mutant Soaked with Uracil and NADPH Anaerobically

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-dimer

Ligands

1 x PRO: PROLINE(Non-covalent)

PRO.1: 2 residues within 4Å: Chain A: L.1017 Ligands: LEU.9 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:L.1017, P.1

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: 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 SF4.4: 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: 13 residues within 4Å: Chain A: 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 A, Metal complexes: A:C.91, A:C.130, A:C.136 SF4.11: 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 SF4.12: 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 SF4.13: 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 SF4.14: 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

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

FAD.6: 32 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, L.310, D.342, T.343, D.346, V.447, G.480, D.481, N.487, T.488, T.489, S.492 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:L.226, A:I.231, A:L.310, A:D.342 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.342, A:D.481, A:N.487, A:T.489, A:T.489, A:S.492, A:S.492 Water bridges: A:S.199, A:Y.222, A:S.227, A:G.284, A:L.285, A:L.285, A:D.444, A:I.482, A:T.489, A:V.490 FAD.15: 32 residues within 4Å: Chain B: 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, L.310, D.342, T.343, D.346, V.447, G.480, D.481, N.487, T.488, T.489, S.492 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:L.226, B:L.310, B:D.342, 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.342, B:D.481, B:N.487, B:T.489, B:T.489, B:S.492 Water bridges: B:S.199, B:K.219, B:K.219, B:L.285, B:L.285, B:I.482, B:T.489, B:V.490

2 x URA: URACIL(Non-covalent)

URA.7: 7 residues within 4Å: Chain A: N.609, E.611, L.612, N.668, N.736, T.737 Ligands: FNR.8 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.609, A:N.609, A:N.668, A:S.670, A:N.736, A:N.736, A:T.737 URA.16: 8 residues within 4Å: Chain B: N.609, E.611, L.612, N.668, S.670, N.736, T.737 Ligands: FNR.17 7 PLIP interactions: 7 interactions with chain B 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 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: 25 residues within 4Å: Chain A: A.549, S.550, A.551, A.552, K.574, T.575, I.590, N.609, E.611, I.613, 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: URA.7 25 PLIP interactions: 25 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:T.575, A:T.575, A:T.575, A:N.668, A:K.709, A:K.709, A:K.709, A:N.736, A:S.766, A:G.767, A:T.793, A:G.795, A:C.816, A:S.817 Water bridges: A:S.550, A:S.640, A:S.640, A:G.794, A:G.794 FNR.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: URA.16 24 PLIP interactions: 24 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: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:G.794

1 x LEU: LEUCINE(Non-covalent)

LEU.9: 4 residues within 4Å: Chain A: L.1017 Chain B: D.579, T.617 Ligands: PRO.1 1 PLIP interactions: 1 interactions with chain B, Hydrophobic interactions: B:T.617

1 x ALA: ALANINE(Non-covalent)

ALA.10: 2 residues within 4Å: Chain A: D.579 Chain B: L.1019 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.1019

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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