MolNFT v1 · #136821 · protein
Saccharomyces cerevisiae old yellow enzyme 3
5V4V · NADPH dehydrogenase 3: “Saccharomyces cerevisiae old yellow enzyme 3”. X-ray diffraction, 2 ligands (FMN, NCA), 3 pockets (best druggability 0.77). MolNFT v1 #136821 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5V4V
- Type
- protein
- Length
- 794 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
- FMN, NCA
- Pockets
- 3 · best druggability 0.77
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 | 397 | 38% helix, 14% strand | P41816 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- NCA · Nicotinamide · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 359 | 0.77 | 0.87 | 48 | FMN, NCA |
| 2 | 359 | 0.77 | 0.87 | 49 | FMN, NCA |
| 3 | 56 | 0.27 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 131 Ų buried · 2 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 5V4V · PDBe 5V4V · UniProt P41816
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