Research workbench
Structure of glycerol-3-phosphate dehydrogenase, GPD1, from sacharomyces cerevisiae
Analyse Structure of glycerol-3-phosphate dehydrogenase, GPD1, from sacharomyces… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FGW
- Type
- protein
- Length
- 706 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerol-3-phosphate dehydrogenase [NAD(+)] 1
- EC
- 1.1.1.8
- UniProt
- Q00055
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glycerol-3-phosphate dehydrogenase [NAD(+)] 1 (EC 1.1.1.8) | protein | 353 | 49% helix, 16% strand | Q00055 |
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 655 | 0.69 | 0.77 | 59 | empty |
| 2 | 581 | 0.66 | 0.76 | 63 | empty |
| 3 | 155 | 0.54 | 0.81 | 23 | empty |
| 4 | 170 | 0.54 | 0.80 | 25 | empty |
| 5 | 74 | 0.45 | 0.82 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1818 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 4FGW · Structure of Glycerol-3-Phosphate Dehydrogenase, GPD1, from Sacharomyces Cerevisiae · the same entry in another collection · chain B against B, TM-score 1.00
- Q00055 · AlphaFold monomer V2.0 prediction for glycerol-3-phosphate dehydrogenase [NAD(+)] 1… · 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 Q00055
- Elsewhere: RCSB PDB 4FGW · PDBe 4FGW · UniProt Q00055
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