MolNFT v1 · #2613 · protein
L-phenylalanine dehydrogenase structure in ternary complex with NAD+ and L-3-phenyllactate
1C1X: “L-phenylalanine dehydrogenase structure in ternary complex with NAD+ and L-3-phenyllactate”. X-ray diffraction, 5 ligands (HFA, NAD, K), 3 pockets (best druggability 0.73). MolNFT v1 #2613 on GenesisL1: 3D structure, binding sites…
- PDB
- 1C1X
- Type
- protein
- Length
- 695 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-phenylalanine dehydrogenase; Protein (L-phenylalanine dehydrogenase)
- UniProt
- Q59771
- Ligands
- HFA, NAD, K, NA, PO4
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-phenylalanine dehydrogenase | protein | 348 | 50% helix, 16% strand | Q59771 |
| B | Protein (L-phenylalanine dehydrogenase) | protein | 347 | 48% helix, 16% strand | Q59771 |
Ligands and binding sites
- HFA · Alpha-hydroxy-beta-phenyl-propionic acid · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · chains A
- PO4 · Phosphate ion · ion · chains B
- IPA · Isopropyl alcohol · additive · 3 copies · chains 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 641 | 0.73 | 0.80 | 76 | K, HFA, NAD |
| 2 | 461 | 0.70 | 0.81 | 54 | K, NAD, HFA |
| 3 | 250 | 0.53 | 0.76 | 42 | empty |
Compared structures
- 1C1X · L-phenylalanine dehydrogenase structure in ternary complex with NAD+ and L-3-phenyllactate · 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 1C1X · PDBe 1C1X · UniProt Q59771
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