MolNFT v1 · #91843 · protein
Crystal structure of recombinant human hexokinase type I mutant D413N glucose 6-phosphate
4FPA · Hexokinase-1: “Crystal structure of recombinant human hexokinase type I mutant D413N glucose 6-phosphate”. X-ray diffraction, 3 ligands (BGC, BG6, NA), 18 pockets (best druggability 0.81). MolNFT v1 #91843 on GenesisL1: 3D…
- PDB
- 4FPA
- 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
- BGC, BG6, NA
- Pockets
- 18 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hexokinase-1 (EC 2.7.1.1) | protein | 899 | 44% helix, 18% strand | P19367 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, B
- BG6 · 6-O-phosphono-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- NA · Sodium ion · metal · 4 copies · chains A, B
- CIT · Citric acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 889 | 0.81 | 0.83 | 104 | BGC, BG6 |
| 2 | 1057 | 0.80 | 0.82 | 115 | BGC, BG6 |
| 3 | 186 | 0.67 | 0.87 | 35 | BGC, BG6 |
| 4 | 446 | 0.63 | 0.76 | 45 | empty |
| 5 | 374 | 0.61 | 0.77 | 51 | empty |
Interfaces
1 interface between chains.
- A–B · 1932 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 4FPA · Crystal Structure of recombinant human Hexokinase type I mutant D413N 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 4FPA · PDBe 4FPA · UniProt P19367
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