Research workbench
Crystal structure of escherichia COLI semet substituted glycerol-3- phosphate dehydrogenase in complex with dhap
Analyse Crystal structure of escherichia COLI semet substituted glycerol-3- phosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R4J
- Type
- protein
- Length
- 991 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
- BCN, FAD, 13P, TAM, PO4
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aerobic glycerol-3-phosphate dehydrogenase (EC 1.1.99.5) | protein | 494 | 37% helix, 25% strand | P13035 |
| B | Aerobic glycerol-3-phosphate dehydrogenase (EC 1.1.99.5) | protein | 497 | 37% helix, 25% strand | P13035 |
Ligands and binding sites
- BCN · Bicine · ligand · 3 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- 13P · 1,3-dihydroxyacetonephosphate · ligand · 2 copies · chains A, B
- TAM · Tris(hydroxyethyl)aminomethane · ligand · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 26 copies · chains A, B
- BOG · octyl beta-D-glucopyranoside · additive · 6 copies · chains A, B
- IMD · Imidazole · additive · 6 copies · chains A, B
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 | 677 | 0.85 | 0.89 | 90 | BOG, FAD, EDO, 13P |
| 2 | 487 | 0.84 | 0.91 | 70 | FAD, EDO, 13P |
| 3 | 1168 | 0.77 | 0.79 | 98 | EDO, IMD, PO4, TAM |
| 4 | 357 | 0.69 | 0.82 | 44 | EDO, IMD |
| 5 | 357 | 0.66 | 0.80 | 46 | EDO |
Interfaces
1 interface between chains.
- A–B · 778 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 2R4J · Crystal structure of Escherichia coli SeMet substituted Glycerol-3-phosphate… · 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 2R4J · PDBe 2R4J · UniProt P13035
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