MolNFT v1 · #91316 · protein
Crystal structure of recombinant human hexokinase type I with 2-deoxy- glucose 6-phosphate
4F9O · Hexokinase-1: “Crystal structure of recombinant human hexokinase type I with 2-deoxy- glucose 6-phosphate”. X-ray diffraction, 3 ligands (0NZ, BGC, NA), 19 pockets (best druggability 0.81). MolNFT v1 #91316 on GenesisL1: 3D…
- PDB
- 4F9O
- Type
- protein
- Length
- 1,798 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hexokinase-1
- EC
- 2.7.1.1
- UniProt
- P19367
- Ligands
- 0NZ, BGC, NA
- Pockets
- 19 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hexokinase-1 (EC 2.7.1.1) | protein | 899 | 44% helix, 19% strand | P19367 |
Ligands and binding sites
- 0NZ · 2-deoxy-6-O-phosphono-beta-D-glucopyranose · ligand · 4 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, B
- NA · Sodium ion · metal · 4 copies · chains A, B
- CIT · Citric acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 942 | 0.81 | 0.83 | 108 | BGC, 0NZ |
| 2 | 906 | 0.81 | 0.83 | 102 | BGC, 0NZ |
| 3 | 186 | 0.66 | 0.86 | 36 | BGC, 0NZ |
| 4 | 154 | 0.61 | 0.85 | 35 | BGC, 0NZ |
| 5 | 422 | 0.61 | 0.76 | 47 | empty |
Interfaces
1 interface between chains.
- A–B · 1954 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 4F9O · Crystal Structure of recombinant human Hexokinase type I with 2-deoxy-Glucose 6-Phosphate · the same entry in another collection · chain A against A, TM-score 1.00
- P19367 · AlphaFold monomer V2.0 prediction for hexokinase-1 (P19367) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P19367
- Elsewhere: RCSB PDB 4F9O · PDBe 4F9O · UniProt P19367
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.