Research workbench
Crystal structure of escherichia COLI glycerol-3-phosphate dehydrogenase in complex with 2-phosphopyruvic acid.
Analyse Crystal structure of escherichia COLI glycerol-3-phosphate dehydrogenase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R46
- Type
- protein
- Length
- 990 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aerobic glycerol-3-phosphate dehydrogenase
- EC
- 1.1.99.5
- UniProt
- P13035
- Ligands
- T3A, FAD, PEP
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aerobic glycerol-3-phosphate dehydrogenase (EC 1.1.99.5) | protein | 495 | 37% helix, 25% strand | P13035 |
Ligands and binding sites
- T3A · N-(tris(hydroxymethyl)methyl)-3-aminopropanesulfonic acid · ligand · 2 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- PEP · Phosphoenolpyruvate · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 22 copies · chains A, B
- BOG · octyl beta-D-glucopyranoside · additive · 5 copies · chains A, B
- IMD · Imidazole · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 517 | 0.84 | 0.90 | 75 | EDO, FAD, PEP |
| 2 | 496 | 0.83 | 0.90 | 71 | EDO, FAD, PEP |
| 3 | 379 | 0.72 | 0.84 | 42 | empty |
| 4 | 365 | 0.68 | 0.82 | 43 | empty |
| 5 | 421 | 0.67 | 0.80 | 45 | empty |
Interfaces
1 interface between chains.
- A–B · 741 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2R46 · Crystal structure of Escherichia coli Glycerol-3-phosphate Dehydrogenase in complex with… · 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 2R46 · PDBe 2R46 · UniProt P13035
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