MolNFT v1 · #181080 · protein
Porcine dihydropyrimidine dehydrogenase (dpd) complexed with 5- ethynyluracil (5EU) - open form
7LJS · Dihydropyrimidine dehydrogenase [NADP(+)]: “Porcine dihydropyrimidine dehydrogenase (dpd) complexed with 5- ethynyluracil (5EU) - open form”. X-ray diffraction, 4 ligands (SF4, FMN, FAD), 20 pockets (best druggability 0.91). MolNFT…
- PDB
- 7LJS
- Type
- protein
- Length
- 4,033 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydropyrimidine dehydrogenase [NADP(+)]
- EC
- 1.3.1.2
- UniProt
- Q28943
- Ligands
- SF4, FMN, FAD, Y3G
- Pockets
- 20 · best druggability 0.91
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydropyrimidine dehydrogenase [NADP(+)] (EC 1.3.1.2) | protein | 1005 | 37% helix, 17% strand | Q28943 |
| B | Dihydropyrimidine dehydrogenase [NADP(+)] (EC 1.3.1.2) | protein | 1004 | 37% helix, 17% strand | Q28943 |
| C | Dihydropyrimidine dehydrogenase [NADP(+)] (EC 1.3.1.2) | protein | 1010 | 37% helix, 17% strand | Q28943 |
| D | Dihydropyrimidine dehydrogenase [NADP(+)] (EC 1.3.1.2) | protein | 1014 | 36% helix, 17% strand | Q28943 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 16 copies · chains A, B, C, D
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- Y3G · 5-ethynylpyrimidine-2,4(1H,3H)-dione · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1134 | 0.91 | 0.94 | 186 | FMN, Y3G |
| 2 | 666 | 0.89 | 0.94 | 120 | FMN, Y3G |
| 3 | 444 | 0.86 | 0.94 | 77 | FMN, Y3G |
| 4 | 982 | 0.85 | 0.86 | 77 | empty |
| 5 | 539 | 0.84 | 0.90 | 69 | FAD |
Interfaces
5 interfaces between chains.
- A–B · 11899 Ų buried · 180 hydrogen bonds · protein-protein
- C–D · 11852 Ų buried · 182 hydrogen bonds · protein-protein
- A–D · 505 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 161 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 91 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7LJS · Porcine Dihydropyrimidine dehydrogenase (DPD) complexed with 5-Ethynyluracil (5EU) - Open… · the same entry in another collection · chain D against D, TM-score 1.00
- Q28943 · AlphaFold monomer V2.0 prediction for dihydropyrimidine dehydrogenase [NADP(+)] (Q28943) · a predicted model of the same protein · chain B against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q28943
- Elsewhere: RCSB PDB 7LJS · PDBe 7LJS · UniProt Q28943
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