MolNFT v1 · #111254 · protein
Insights into flavin-based electron bifurcation via the NADH-dependent reduced ferredoxin-NADP oxidoreductase structure
4YLF · Dihydroorotate dehydrogenase B (NAD(+)), electron transfer…: “Insights into flavin-based electron bifurcation via the NADH-dependent reduced ferredoxin-NADP oxidoreductase…”. X-ray diffraction, 4 ligands (FAD, SF4, FES), 20 pockets…
- PDB
- 4YLF
- Type
- protein
- Length
- 1,475 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog…
- UniProt
- Q9X1X4, V9X7T9
- Ligands
- FAD, SF4, FES, PO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog | protein | 276 | 22% helix, 30% strand | Q9X1X4 |
| B, D | Dihydropyrimidine dehydrogenase subunit a | protein | 468 | 34% helix, 17% strand | V9X7T9 |
| C | Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog | protein | 263 | 20% helix, 29% strand | Q9X1X4 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains B, D
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A, C
- PO4 · Phosphate ion · ion · 2 copies · chains B, 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 902 | 0.84 | 0.85 | 121 | FAD |
| 2 | 1066 | 0.81 | 0.82 | 104 | FAD |
| 3 | 728 | 0.80 | 0.84 | 48 | FAD |
| 4 | 760 | 0.79 | 0.83 | 53 | FAD |
| 5 | 812 | 0.75 | 0.79 | 84 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1865 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1841 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 849 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 244 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 138 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4YLF · Insights into flavin-based electron bifurcation via the NADH-dependent reduced… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9X1X4 · AlphaFold monomer V2.0 prediction for dihydroorotate dehydrogenase B (NAD(+)), electron… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9X1X4
- Every structure of UniProt V9X7T9
- Elsewhere: RCSB PDB 4YLF · PDBe 4YLF · UniProt Q9X1X4 · UniProt V9X7T9
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