Research workbench
2.7 ångström crystal structure of glycerol kinase (glpk) from staphylococcus aureus in complex with ADP and glycerol
Analyse 2.7 ångström crystal structure of glycerol kinase (glpk) from staphylococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GE1
- Type
- protein
- Length
- 1,990 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerol kinase
- EC
- 2.7.1.30
- UniProt
- Q5HGD2
- Ligands
- ADP, PO4, CL
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycerol kinase (EC 2.7.1.30) | protein | 499 | 35% helix, 25% strand | Q5HGD2 |
| B | Glycerol kinase (EC 2.7.1.30) | protein | 498 | 37% helix, 24% strand | Q5HGD2 |
| C | Glycerol kinase (EC 2.7.1.30) | protein | 497 | 36% helix, 25% strand | Q5HGD2 |
| D | Glycerol kinase (EC 2.7.1.30) | protein | 496 | 36% helix, 24% strand | Q5HGD2 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.73 | 0.93 | 30 | empty |
| 2 | 424 | 0.72 | 0.83 | 46 | ADP, GOL |
| 3 | 387 | 0.72 | 0.83 | 46 | ADP, GOL |
| 4 | 414 | 0.71 | 0.83 | 47 | ADP, GOL |
| 5 | 397 | 0.70 | 0.82 | 45 | ADP, GOL |
Interfaces
4 interfaces between chains.
- A–B · 1916 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1848 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 836 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 777 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 43 modified (engineered).
Compared structures
- 3GE1 · 2.7 Angstrom Crystal Structure of Glycerol Kinase (glpK) from Staphylococcus aureus in… · the same entry in another collection · chain D against D, TM-score 1.00
- Q5HGD2 · AlphaFold monomer V2.0 prediction for glycerol kinase (Q5HGD2) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 Q5HGD2
- Elsewhere: RCSB PDB 3GE1 · PDBe 3GE1 · UniProt Q5HGD2
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