MolNFT v1 · #82493 · protein
Crystal structure of rok hexokinase from thermus thermophilus
3VOV · Glucokinase: “Crystal structure of rok hexokinase from thermus thermophilus”. X-ray diffraction, 1 ligand (ZN), 13 pockets (best druggability 0.73). MolNFT v1 #82493 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3VOV
- Type
- protein
- Length
- 1,180 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucokinase
- EC
- 2.7.1.1
- UniProt
- Q5SLJ4
- Ligands
- ZN
- Pockets
- 13 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucokinase (EC 2.7.1.1) | protein | 297 | 44% helix, 20% strand | Q5SLJ4 |
| B | Glucokinase (EC 2.7.1.1) | protein | 298 | 44% helix, 20% strand | Q5SLJ4 |
| C | Glucokinase (EC 2.7.1.1) | protein | 289 | 44% helix, 20% strand | Q5SLJ4 |
| D | Glucokinase (EC 2.7.1.1) | protein | 296 | 43% helix, 20% strand | Q5SLJ4 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 371 | 0.73 | 0.84 | 29 | GOL |
| 2 | 364 | 0.72 | 0.84 | 34 | GOL |
| 3 | 609 | 0.66 | 0.76 | 64 | empty |
| 4 | 594 | 0.65 | 0.76 | 62 | empty |
| 5 | 580 | 0.65 | 0.76 | 60 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1831 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 1819 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 1153 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1140 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 304 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3VOV · Crystal Structure of ROK Hexokinase from Thermus thermophilus · the same entry in another collection · chain A 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 Q5SLJ4
- Elsewhere: RCSB PDB 3VOV · PDBe 3VOV · UniProt Q5SLJ4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.