Research workbench
Porcine dihydropyrimidine dehydrogenase (dpd) crosslinked with 5- ethynyluracil (5EU)
Analyse Porcine dihydropyrimidine dehydrogenase (dpd) crosslinked with 5- ethynyluracil… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LJU
- Type
- protein
- Length
- 4,041 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, FAD, Y3G, NAP, FNR
- Pockets
- 20 · best druggability 0.91
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydropyrimidine dehydrogenase [NADP(+)] (EC 1.3.1.2) | protein | 1016 | 36% helix, 17% strand | Q28943 |
| C, B | Dihydropyrimidine dehydrogenase [NADP(+)] (EC 1.3.1.2) | protein | 1004 | 36% helix, 17% strand | Q28943 |
| D | Dihydropyrimidine dehydrogenase [NADP(+)] (EC 1.3.1.2) | protein | 1017 | 36% helix, 17% strand | Q28943 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 16 copies · chains A, C, D, B
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, C, D, B
- Y3G · 5-ethynylpyrimidine-2,4(1H,3H)-dione · ligand · 4 copies · chains A, C, D, B
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, C, D, B
- 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 · ligand · 4 copies · chains A, C, D, B
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 | 1141 | 0.91 | 0.94 | 194 | Y3G, FNR |
| 2 | 637 | 0.89 | 0.94 | 106 | Y3G, FNR |
| 3 | 490 | 0.87 | 0.94 | 79 | FNR, Y3G |
| 4 | 565 | 0.83 | 0.89 | 70 | FAD |
| 5 | 702 | 0.83 | 0.87 | 87 | FAD, NAP |
Interfaces
5 interfaces between chains.
- C–D · 11928 Ų buried · 186 hydrogen bonds · protein-protein
- A–B · 11864 Ų buried · 187 hydrogen bonds · protein-protein
- A–D · 554 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 99 Ų buried · 0 hydrogen bonds · protein-protein
- D–B · 87 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7LJU · Porcine Dihydropyrimidine Dehydrogenase (DPD) crosslinked with 5-Ethynyluracil (5EU) · the same entry in another collection · chain B against B, 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 7LJU · PDBe 7LJU · UniProt Q28943
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