Research workbench
Pyrococcus furiosus galactokinase in complex with galactose, ADP and magnesium
Analyse Pyrococcus furiosus galactokinase in complex with galactose, ADP and magnesium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1S4E
- Type
- protein
- Length
- 2,983 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galactokinase
- EC
- 2.7.1.6
- UniProt
- Q9HHB6
- Ligands
- ADP, GLA, MG
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 8 distinct chains · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Galactokinase (EC 2.7.1.6) | protein | 337 | 46% helix, 20% strand | Q9HHB6 |
| B | Galactokinase (EC 2.7.1.6) | protein | 310 | 47% helix, 20% strand | Q9HHB6 |
| C | Galactokinase (EC 2.7.1.6) | protein | 337 | 42% helix, 25% strand | Q9HHB6 |
| D | Galactokinase (EC 2.7.1.6) | protein | 349 | 44% helix, 26% strand | Q9HHB6 |
| E | Galactokinase (EC 2.7.1.6) | protein | 346 | 42% helix, 24% strand | Q9HHB6 |
| F, I | Galactokinase (EC 2.7.1.6) | protein | 351 | 43% helix, 25% strand | Q9HHB6 |
| G | Galactokinase (EC 2.7.1.6) | protein | 255 | 48% helix, 11% strand | Q9HHB6 |
| H | Galactokinase (EC 2.7.1.6) | protein | 347 | 45% helix, 24% strand | Q9HHB6 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 9 copies · chains A, B, C, D, E, F, G, H, I
- GLA · alpha-D-galactopyranose · sugar · 9 copies · chains A, B, C, D, E, F, G, H, I
- MG · Magnesium ion · metal · 9 copies · chains A, B, C, D, E, F, G, H, I
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 | 503 | 0.74 | 0.83 | 52 | GLA, MG, ADP |
| 2 | 527 | 0.74 | 0.82 | 53 | GLA, MG, ADP |
| 3 | 503 | 0.74 | 0.82 | 55 | GLA, MG, ADP |
| 4 | 503 | 0.73 | 0.82 | 58 | GLA, MG, ADP |
| 5 | 981 | 0.73 | 0.77 | 98 | empty |
Interfaces
7 interfaces between chains.
- H–I · 567 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 539 Ų buried · 5 hydrogen bonds · protein-protein
- A–F · 471 Ų buried · 3 hydrogen bonds · protein-protein
- F–H · 428 Ų buried · 2 hydrogen bonds · protein-protein
- C–E · 378 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 modified (engineered).
Compared structures
- 1S4E · Pyrococcus furiosus galactokinase in complex with galactose, ADP and magnesium · the same entry in another collection · chain I against I, TM-score 1.00
- Q9HHB6 · AlphaFold monomer V2.0 prediction for galactokinase (Q9HHB6) · a predicted model of the same protein · chain E against A, TM-score 1.00
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 Q9HHB6
- Elsewhere: RCSB PDB 1S4E · PDBe 1S4E · UniProt Q9HHB6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.