Research workbench
Crystal structure of recombinant human hexokinase type I with 1,5- anhydroglucitol 6-phosphate
Analyse Crystal structure of recombinant human hexokinase type I with 1,5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FPB
- 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
- 0WK, BGC, NA
- Pockets
- 18 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hexokinase-1 (EC 2.7.1.1) | protein | 899 | 46% helix, 18% strand | P19367 |
Ligands and binding sites
- 0WK · 1,5-anhydro-6-O-phosphono-D-glucitol · 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 · 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 | 807 | 0.79 | 0.83 | 89 | BGC, 0WK |
| 2 | 723 | 0.79 | 0.84 | 89 | BGC, 0WK |
| 3 | 187 | 0.66 | 0.86 | 36 | BGC, 0WK |
| 4 | 360 | 0.60 | 0.77 | 51 | empty |
| 5 | 453 | 0.60 | 0.75 | 51 | empty |
Interfaces
1 interface between chains.
- A–B · 2026 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 4FPB · Crystal Structure of Recombinant Human Hexokinase Type I with 1,5-Anhydroglucitol… · 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 4FPB · PDBe 4FPB · UniProt P19367
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