MolNFT v1 · #8176 · protein
Dihydropyrimidine dehydrogenase (dpd) from pig, ternary complex with NADPH and uracil-4-acetic acid
1GT8: “Dihydropyrimidine dehydrogenase (dpd) from pig, ternary complex with NADPH and uracil-4-acetic acid”. X-ray diffraction, 5 ligands (SF4, FMN, FAD), 20 pockets (best druggability 0.91). MolNFT v1 #8176 on GenesisL1: 3D structure…
- PDB
- 1GT8
- Type
- protein
- Length
- 4,049 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydropyrimidine dehydrogenase
- EC
- 1.3.1.2
- UniProt
- Q28943
- Ligands
- SF4, FMN, FAD, NDP, UAA
- Pockets
- 20 · best druggability 0.91
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydropyrimidine dehydrogenase (EC 1.3.1.2) | protein | 1017 | 35% helix, 16% strand | Q28943 |
| B | Dihydropyrimidine dehydrogenase (EC 1.3.1.2) | protein | 1010 | 36% helix, 17% strand | Q28943 |
| C | Dihydropyrimidine dehydrogenase (EC 1.3.1.2) | protein | 1010 | 35% helix, 16% strand | Q28943 |
| D | Dihydropyrimidine dehydrogenase (EC 1.3.1.2) | protein | 1012 | 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
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- UAA · Uracil-6-acetic acid · 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 | 1135 | 0.91 | 0.94 | 194 | FMN, UAA |
| 2 | 519 | 0.87 | 0.93 | 87 | FMN, UAA |
| 3 | 468 | 0.86 | 0.93 | 74 | FMN, UAA |
| 4 | 614 | 0.83 | 0.88 | 74 | FAD |
| 5 | 702 | 0.83 | 0.87 | 93 | FAD, NDP |
Interfaces
4 interfaces between chains.
- A–B · 12070 Ų buried · 185 hydrogen bonds · protein-protein
- C–D · 12009 Ų buried · 191 hydrogen bonds · protein-protein
- A–D · 356 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 183 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1GT8 · Dihydropyrimidine dehydrogenase (dpd) from pig, ternary complex with NADPH and… · the same entry in another collection · chain C against C, TM-score 1.00
- Q28943 · AlphaFold monomer V2.0 prediction for dihydropyrimidine dehydrogenase [NADP(+)] (Q28943) · a predicted model of the same protein · chain C 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 1GT8 · PDBe 1GT8 · UniProt Q28943
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