Research workbench
Dihydropyrimidine dehydrogenase (dpd) from pig, ternary complex with NADPH and 5-iodouracil
Analyse Dihydropyrimidine dehydrogenase (dpd) from pig, ternary complex with NADPH and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GTH
- Type
- protein
- Length
- 4,065 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, IDH, IUR, URA
- Pockets
- 20 · best druggability 0.91
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Dihydropyrimidine dehydrogenase (EC 1.3.1.2) | protein | 1019 | 35% helix, 16% strand | Q28943 |
| B | Dihydropyrimidine dehydrogenase (EC 1.3.1.2) | protein | 1012 | 36% helix, 16% strand | Q28943 |
| C | Dihydropyrimidine dehydrogenase (EC 1.3.1.2) | protein | 1015 | 37% 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
- IDH · (5S)-5-iododihydro-2,4(1H,3H)-pyrimidinedione · ligand · 2 copies · chains A, B
- IUR · 5-iodouracil · ligand · chains C
- URA · Uracil · ligand · chains 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 | 786 | 0.91 | 0.96 | 152 | FMN, IDH |
| 2 | 537 | 0.89 | 0.96 | 100 | FMN, IUR |
| 3 | 362 | 0.87 | 0.96 | 76 | FMN, URA |
| 4 | 1011 | 0.85 | 0.86 | 83 | empty |
| 5 | 697 | 0.84 | 0.88 | 87 | FAD, NDP |
Interfaces
4 interfaces between chains.
- A–B · 12178 Ų buried · 188 hydrogen bonds · protein-protein
- C–D · 12146 Ų buried · 185 hydrogen bonds · protein-protein
- A–D · 424 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 205 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1GTH · Dihydropyrimidine dehydrogenase (dpd) from pig, ternary complex with NADPH and… · 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 1GTH · PDBe 1GTH · UniProt Q28943
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