Research workbench
Unliganded human glycerol 3-phosphate dehydrogenase
Analyse Unliganded human glycerol 3-phosphate dehydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E8Y
- Type
- protein
- Length
- 684 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
- 3SY, K, PO4
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycerol-3-phosphate dehydrogenase [NAD(+)], cytoplasmic (EC 1.1.1.8) | protein | 344 | 54% helix, 15% strand | P21695 |
| B | Glycerol-3-phosphate dehydrogenase [NAD(+)], cytoplasmic (EC 1.1.1.8) | protein | 340 | 55% helix, 13% strand | P21695 |
Ligands and binding sites
- 3SY · 2,2-bis(hydroxymethyl)propane-1,3-diol · ligand · chains A
- K · Potassium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 523 | 0.63 | 0.76 | 44 | empty |
| 2 | 510 | 0.62 | 0.75 | 50 | empty |
Interfaces
1 interface between chains.
- A–B · 1886 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
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 6E8Y · PDBe 6E8Y · UniProt P21695
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