MolNFT v1 · #154310 · protein
Glycerol kinase form thermococcus kodakarensis, complex structure with substrate.
6K79: “Glycerol kinase form thermococcus kodakarensis, complex structure with substrate.”. X-ray diffraction, 16 pockets (best druggability 0.82). MolNFT v1 #154310 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6K79
- Type
- protein
- Length
- 1,961 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerol kinase
- EC
- 2.7.1.30
- UniProt
- O93623
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 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 A against A, 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
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