Research workbench
Phenylalanine dehydrogenase structure in ternary complex with NAD+ and phenylpyruvate
Analyse Phenylalanine dehydrogenase structure in ternary complex with NAD+ and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BW9
- Type
- protein
- Length
- 697 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenylalanine dehydrogenase
- EC
- 1.4.1.20
- UniProt
- Q59771
- Ligands
- NAD, PPY, K, NA, PO4
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenylalanine dehydrogenase (EC 1.4.1.20) | protein | 350 | 48% helix, 16% strand | Q59771 |
| B | Phenylalanine dehydrogenase (EC 1.4.1.20) | protein | 347 | 48% helix, 17% strand | Q59771 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- PPY · 3-phenylpyruvic acid · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains B
- PO4 · Phosphate ion · ion · chains B
- IPA · Isopropyl alcohol · additive · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 615 | 0.73 | 0.80 | 81 | NAD, PPY, K, EDO |
| 2 | 448 | 0.70 | 0.81 | 50 | NAD, PPY |
| 3 | 286 | 0.56 | 0.77 | 45 | IPA |
Compared structures
- 1BW9 · Phenylalanine dehydrogenase structure in ternary complex with NAD+ and phenylpyruvate · the same entry in another collection · chain A against A, TM-score 1.00
- Q59771 · AlphaFold monomer V2.0 prediction for phenylalanine dehydrogenase (Q59771) · a predicted model of the same protein · chain B 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 Q59771
- Elsewhere: RCSB PDB 1BW9 · PDBe 1BW9 · UniProt Q59771
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.