Research workbench
Dihydropyrimidine dehydrogenase (dpd) from pig, binary complex with 5- iodouracil
Analyse Dihydropyrimidine dehydrogenase (dpd) from pig, binary complex with 5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GTE
- Type
- protein
- Length
- 4,034 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, IUR
- Pockets
- 20 · best druggability 0.91
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydropyrimidine dehydrogenase (EC 1.3.1.2) | protein | 1005 | 36% helix, 17% strand | Q28943 |
| B | Dihydropyrimidine dehydrogenase (EC 1.3.1.2) | protein | 1005 | 36% helix, 17% strand | Q28943 |
| C | Dihydropyrimidine dehydrogenase (EC 1.3.1.2) | protein | 1010 | 36% helix, 17% strand | Q28943 |
| D | Dihydropyrimidine dehydrogenase (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
- IUR · 5-iodouracil · 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 | 1090 | 0.91 | 0.94 | 171 | FMN, IUR |
| 2 | 605 | 0.88 | 0.94 | 97 | FMN, IUR |
| 3 | 452 | 0.86 | 0.94 | 80 | FMN, IUR |
| 4 | 557 | 0.84 | 0.90 | 66 | FAD |
| 5 | 646 | 0.84 | 0.88 | 82 | FAD |
Interfaces
6 interfaces between chains.
- C–D · 11819 Ų buried · 181 hydrogen bonds · protein-protein
- A–B · 11743 Ų buried · 177 hydrogen bonds · protein-protein
- A–D · 546 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 183 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 85 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1GTE · Dihydropyrimidine dehydrogenase (dpd) from pig, binary complex with 5-iodouracil · 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 1GTE · PDBe 1GTE · UniProt Q28943
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.