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Crystal structure of Glycerol-3-phosphate Dehydrogenase from Escherichia coli
Analyse Crystal structure of Glycerol-3-phosphate Dehydrogenase from Escherichia coli in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QCU
- Type
- protein
- Length
- 1,000 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.75
- Source
- Escherichia coli
- Molecule
- Aerobic glycerol-3-phosphate dehydrogenase
- EC
- 1.1.99.5
- UniProt
- P13035
- Ligands
- TAM, FAD, SO4, PO4
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · resolution 1.75 · 2 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aerobic glycerol-3-phosphate dehydrogenase (EC 1.1.99.5) | protein | 499 | 38% helix, 24% strand | P13035 |
| B | Aerobic glycerol-3-phosphate dehydrogenase (EC 1.1.99.5) | protein | 501 | 37% helix, 24% strand | P13035 |
Ligands and binding sites
- TAM · Tris(hydroxyethyl)aminomethane · ligand · 3 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 30 copies · chains A, B
- BOG · octyl beta-D-glucopyranoside · additive · 6 copies · chains A, B
- IMD · Imidazole · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 609 | 0.85 | 0.90 | 88 | PO4, FAD, EDO |
| 2 | 509 | 0.84 | 0.90 | 68 | PO4, FAD, EDO |
| 3 | 961 | 0.75 | 0.78 | 75 | SO4, TAM, EDO |
| 4 | 348 | 0.72 | 0.84 | 41 | EDO |
| 5 | 411 | 0.72 | 0.83 | 48 | SO4, IMD, EDO |
Interfaces
1 interface between chains.
- A–B · 866 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 2QCU · Crystal structure of glycerol-3-phosphate dehydrogenase from escherichia COLI · the same entry in another collection · chain A against A, TM-score 1.00
- P13035 · AlphaFold monomer V2.0 prediction for aerobic glycerol-3-phosphate dehydrogenase (P13035) · 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 P13035
- Elsewhere: RCSB PDB 2QCU · PDBe 2QCU · UniProt P13035
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