MolNFT v1 · #64799 · protein
2.7 ångström crystal structure of glycerol kinase (glpk) from staphylococcus aureus in complex with ADP and glycerol
3GE1: “2.7 ångström crystal structure of glycerol kinase (glpk) from staphylococcus aureus in complex with ADP and…”. X-ray diffraction, 3 ligands (ADP, PO4, CL), 20 pockets (best druggability 0.73). MolNFT v1 #64799 on GenesisL1: 3D…
- 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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