Research workbench
Glycerol kinase form Thermococcus kodakarensis, complex structure with substrate.
Analyse Glycerol kinase form Thermococcus kodakarensis, complex structure with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K79
- Type
- protein
- Length
- 1,961 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.19
- Source
- Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
- Molecule
- Glycerol kinase
- EC
- 2.7.1.30
- UniProt
- O93623
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.19 · 3 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Glycerol kinase (EC 2.7.1.30) | protein | 490 | 39% helix, 24% strand | O93623 |
| C, A | Glycerol kinase (EC 2.7.1.30) | protein | 490 | 38% helix, 24% strand | O93623 |
| D | Glycerol kinase (EC 2.7.1.30) | protein | 491 | 37% helix, 24% strand | O93623 |
Ligands and binding sites
- PGE · Triethylene glycol · additive · 4 copies · chains B, C, D, A
- GOL · Glycerol · additive · 4 copies · chains B, C, D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1064 | 0.82 | 0.83 | 91 | empty |
| 2 | 716 | 0.74 | 0.79 | 70 | PGE, GOL |
| 3 | 700 | 0.73 | 0.79 | 70 | PGE, GOL |
| 4 | 717 | 0.73 | 0.79 | 72 | PGE, GOL |
| 5 | 719 | 0.72 | 0.78 | 67 | PGE, GOL |
Interfaces
5 interfaces between chains.
- B–C · 590 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 270 Ų buried · 9 hydrogen bonds · protein-protein
- C–A · 255 Ų buried · 0 hydrogen bonds · protein-protein
- B–A · 238 Ų buried · 6 hydrogen bonds · protein-protein
- D–A · 56 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6K79 · Glycerol kinase form thermococcus kodakarensis, complex structure with substrate. · the same entry in another collection · chain D against D, TM-score 1.00
- O93623 · AlphaFold monomer V2.0 prediction for glycerol kinase (O93623) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 O93623
- Elsewhere: RCSB PDB 6K79 · PDBe 6K79 · UniProt O93623
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.