Research workbench
Structure of glycerophosphate dehydrogenase in complex with NADPH
Analyse Structure of glycerophosphate dehydrogenase in complex with NADPH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FB3
- Type
- protein
- Length
- 2,008 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerol-1-phosphate dehydrogenase [NAD(P)+]
- EC
- 1.1.1.261
- UniProt
- A3MTM6
- Ligands
- NDP, PPV, ZN, SO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Glycerol-1-phosphate dehydrogenase [NAD(P)+] (EC 1.1.1.261) | protein | 336 | 53% helix, 10% strand | A3MTM6 |
| B | Glycerol-1-phosphate dehydrogenase [NAD(P)+] (EC 1.1.1.261) | protein | 329 | 52% helix, 9% strand | A3MTM6 |
| E | Glycerol-1-phosphate dehydrogenase [NAD(P)+] (EC 1.1.1.261) | protein | 334 | 55% helix, 11% strand | A3MTM6 |
| F | Glycerol-1-phosphate dehydrogenase [NAD(P)+] (EC 1.1.1.261) | protein | 337 | 56% helix, 10% strand | A3MTM6 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 3 copies · chains D, E, F
- PPV · Pyrophosphate · ligand · chains B
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, D, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1140 | 0.79 | 0.81 | 120 | SO4 |
| 2 | 245 | 0.77 | 0.90 | 39 | SO4 |
| 3 | 535 | 0.75 | 0.83 | 62 | NDP, SO4 |
| 4 | 738 | 0.75 | 0.80 | 79 | empty |
| 5 | 560 | 0.75 | 0.82 | 65 | NDP |
Interfaces
11 interfaces between chains.
- E–F · 1682 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 1640 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1630 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 965 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 901 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5FB3 · Structure of glycerophosphate dehydrogenase in complex with NADPH · the same entry in another collection · chain F against F, TM-score 1.00
- A3MTM6 · AlphaFold monomer V2.0 prediction for glycerol-1-phosphate dehydrogenase [NAD(P)+]… · a predicted model of the same protein · chain F 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 A3MTM6
- Elsewhere: RCSB PDB 5FB3 · PDBe 5FB3 · UniProt A3MTM6
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