Research workbench
Ternary complex of human glycerol 3-phosphate dehydrogenase
Analyse Ternary complex of 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
- 6E90
- Type
- protein
- Length
- 1,369 residues
- Chains
- 4
- 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
- NAD, 13P, CA, PO4
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 15% 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 | 345 | 54% helix, 15% strand | P21695 |
| C | Glycerol-3-phosphate dehydrogenase [NAD(+)], cytoplasmic (EC 1.1.1.8) | protein | 344 | 53% helix, 16% strand | P21695 |
| D | Glycerol-3-phosphate dehydrogenase [NAD(+)], cytoplasmic (EC 1.1.1.8) | protein | 336 | 54% helix, 13% strand | P21695 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 3 copies · chains A, B, C
- 13P · 1,3-dihydroxyacetonephosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 420 | 0.77 | 0.86 | 47 | NAD, 13P |
| 2 | 371 | 0.76 | 0.86 | 48 | NAD, 13P |
| 3 | 863 | 0.74 | 0.78 | 102 | CA |
| 4 | 654 | 0.74 | 0.80 | 64 | PO4 |
| 5 | 501 | 0.69 | 0.79 | 55 | PO4 |
Interfaces
4 interfaces between chains.
- A–C · 1784 Ų buried · 37 hydrogen bonds · protein-protein
- B–D · 636 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 484 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 321 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6E90 · Ternary complex of human glycerol 3-phosphate dehydrogenase · the same entry in another collection · chain D against D, 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 0.99
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 P21695
- Elsewhere: RCSB PDB 6E90 · PDBe 6E90 · UniProt P21695
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