Research workbench
L-phenylalanine dehydrogenase structure in ternary complex with NADH and L-phenylalanine
Analyse L-phenylalanine dehydrogenase structure in ternary complex with NADH and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1C1D
- Type
- protein
- Length
- 697 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-phenylalanine dehydrogenase
- UniProt
- Q59771
- Ligands
- PHE, NAI, K, NA, PO4
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-phenylalanine dehydrogenase | protein | 349 | 50% helix, 17% strand | Q59771 |
| B | L-phenylalanine dehydrogenase | protein | 348 | 48% helix, 16% strand | Q59771 |
Ligands and binding sites
- PHE · Phenylalanine · ligand · 2 copies · chains A, B
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains B
- PO4 · Phosphate ion · ion · chains B
- IPA · Isopropyl alcohol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 377 | 0.72 | 0.83 | 47 | K, PHE, NAI |
| 2 | 439 | 0.70 | 0.81 | 51 | K, PHE, NAI |
| 3 | 285 | 0.56 | 0.77 | 44 | empty |
| 4 | 155 | 0.48 | 0.78 | 23 | empty |
Compared structures
- 1C1D · L-phenylalanine dehydrogenase structure in ternary complex with NADH and L-phenylalanine · 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 0.99
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 1C1D · PDBe 1C1D · UniProt Q59771
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