MolNFT v1 · #136815 · protein
Saccharomyces cerevisiae oye 3 soaked with P-hydroxybenzaldehyde
5V4P · NADPH dehydrogenase 3: “Saccharomyces cerevisiae oye 3 soaked with P-hydroxybenzaldehyde”. X-ray diffraction, 4 ligands (TOE, FMN, HBA), 2 pockets (best druggability 0.79). MolNFT v1 #136815 on GenesisL1: 3D structure, binding sites…
- PDB
- 5V4P
- Type
- protein
- Length
- 792 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADPH dehydrogenase 3
- EC
- 1.6.99.1
- UniProt
- P41816
- Ligands
- TOE, FMN, HBA, NA
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NADPH dehydrogenase 3 (EC 1.6.99.1) | protein | 396 | 38% helix, 14% strand | P41816 |
Ligands and binding sites
- TOE · 2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxyl · ligand · 4 copies · chains A, B
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- HBA · P-hydroxybenzaldehyde · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 340 | 0.79 | 0.89 | 51 | FMN, HBA |
| 2 | 345 | 0.79 | 0.89 | 49 | FMN, HBA |
Interfaces
1 interface between chains.
- A–B · 143 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
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 P41816
- Elsewhere: RCSB PDB 5V4P · PDBe 5V4P · UniProt P41816
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