MolNFT v1 · #140789 · protein
Crystal structure of the cytochrome B5 reductase domain of ulva prolifera nitrate reductase
5YLY: “Crystal structure of the cytochrome B5 reductase domain of ulva prolifera nitrate reductase”. X-ray diffraction, 1 ligand (FAD), 6 pockets (best druggability 0.63). MolNFT v1 #140789 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5YLY
- Type
- protein
- Length
- 531 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrate reductase
- Ligands
- FAD
- Pockets
- 6 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrate reductase | protein | 262 | 22% helix, 36% strand | — |
| B | Nitrate reductase | protein | 269 | 21% helix, 36% strand | — |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 434 | 0.63 | 0.77 | 48 | FAD |
| 2 | 411 | 0.60 | 0.76 | 49 | FAD |
| 3 | 191 | 0.46 | 0.74 | 31 | empty |
| 4 | 97 | 0.40 | 0.77 | 18 | empty |
| 5 | 64 | 0.36 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 405 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5YLY · Crystal structure of the cytochrome b5 reductase domain of Ulva prolifera nitrate… · 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
- Elsewhere: RCSB PDB 5YLY · PDBe 5YLY
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