Research workbench
Ternary complex of glycerol 3-phosphate dehydrogenase 1 with NAD and dihydroxyactone
Analyse Ternary complex of glycerol 3-phosphate dehydrogenase 1 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
- 1WPQ
- Type
- protein
- Length
- 696 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerol-3-phosphate dehydrogenase [NAD+], cytoplasmic
- EC
- 1.1.1.8
- UniProt
- P21695
- Ligands
- 13P, NAD, SO4
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glycerol-3-phosphate dehydrogenase [NAD+], cytoplasmic (EC 1.1.1.8) | protein | 348 | 53% helix, 16% strand | P21695 |
Ligands and binding sites
- 13P · 1,3-dihydroxyacetonephosphate · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 428 | 0.81 | 0.89 | 49 | 13P, NAD |
| 2 | 463 | 0.81 | 0.88 | 55 | 13P, NAD |
| 3 | 51 | 0.46 | 0.85 | 18 | empty |
| 4 | 75 | 0.43 | 0.80 | 15 | empty |
| 5 | 67 | 0.40 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1819 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 1WPQ · Ternary Complex Of Glycerol 3-phosphate Dehydrogenase 1 with NAD and dihydroxyactone · the same entry in another collection · chain A against A, TM-score 1.00
- P21695 · AlphaFold monomer V2.0 prediction for glycerol-3-phosphate dehydrogenase [NAD(+)]… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P21695
- Elsewhere: RCSB PDB 1WPQ · PDBe 1WPQ · UniProt P21695
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