Research workbench
Crystal structure of homo sapien glycerol-3-phosphate dehydrogenase 1
Analyse Crystal structure of homo sapien glycerol-3-phosphate dehydrogenase 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1X0V
- Type
- protein
- Length
- 697 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
- SO4
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycerol-3-phosphate dehydrogenase [NAD+], cytoplasmic (EC 1.1.1.8) | protein | 348 | 53% helix, 14% strand | P21695 |
| B | Glycerol-3-phosphate dehydrogenase [NAD+], cytoplasmic (EC 1.1.1.8) | protein | 349 | 53% helix, 14% strand | P21695 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 14 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 | 447 | 0.80 | 0.88 | 47 | SO4 |
| 2 | 319 | 0.76 | 0.88 | 48 | SO4 |
| 3 | 66 | 0.49 | 0.84 | 17 | empty |
| 4 | 85 | 0.42 | 0.79 | 15 | empty |
| 5 | 112 | 0.42 | 0.77 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1819 Ų buried · 41 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 modified (engineered).
Compared structures
- 1X0V · Crystal Structure of Homo Sapien Glycerol-3-Phosphate Dehydrogenase 1 · 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 B 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 1X0V · PDBe 1X0V · UniProt P21695
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.