MolNFT v1 · #135950 · protein
Wt dhodb with orotate bound
5UE9 · Dihydroorotate dehydrogenase: “Wt dhodb with orotate bound”. X-ray diffraction, 5 ligands (FMN, ORO, FAD), 13 pockets (best druggability 0.78). MolNFT v1 #135950 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5UE9
- Type
- protein
- Length
- 1,135 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroorotate dehydrogenase; Dihydroorotate dehydrogenase B (NAD(+)), electron transfer…
- EC
- 1.3.1.14
- UniProt
- A0A0V8EUT4, A0A0V8EGX5
- Ligands
- FMN, ORO, FAD, FES, CL
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotate dehydrogenase (EC 1.3.1.14) | protein | 306 | 38% helix, 22% strand | A0A0V8EUT4 |
| B, D | Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit | protein | 262 | 19% helix, 34% strand | A0A0V8EGX5 |
| C | Dihydroorotate dehydrogenase (EC 1.3.1.14) | protein | 305 | 37% helix, 22% strand | A0A0V8EUT4 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B, D, C
- ORO · Orotic acid · ligand · 2 copies · chains A, C
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B, D, C
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains B, D
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 2 copies · chains B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 787 | 0.78 | 0.82 | 88 | FMN, ORO, GOL |
| 2 | 405 | 0.75 | 0.85 | 51 | FMN, ORO |
| 3 | 823 | 0.74 | 0.79 | 103 | empty |
| 4 | 557 | 0.69 | 0.78 | 38 | FAD |
| 5 | 496 | 0.67 | 0.78 | 41 | FAD |
Interfaces
5 interfaces between chains.
- D–C · 1433 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1357 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 454 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 287 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 53 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5UE9 · WT DHODB with orotate bound · the same entry in another collection · chain A 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 A0A0V8EUT4
- Every structure of UniProt A0A0V8EGX5
- Elsewhere: RCSB PDB 5UE9 · PDBe 5UE9 · UniProt A0A0V8EUT4 · UniProt A0A0V8EGX5
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