MolNFT v1 · #1907 · protein
Rat brain hexokinase type I complex with glucose and inhibitor glucose-6-phosphate
1BG3: “Rat brain hexokinase type I complex with glucose and inhibitor glucose-6-phosphate”. X-ray diffraction, 3 ligands (BGC, G6P, CA), 17 pockets (best druggability 0.77). MolNFT v1 #1907 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1BG3
- Type
- protein
- Length
- 1,804 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hexokinase
- EC
- 2.7.1.1
- UniProt
- P05708
- Ligands
- BGC, G6P, CA
- Pockets
- 17 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hexokinase (EC 2.7.1.1) | protein | 902 | 47% helix, 17% strand | P05708 |
| B | Hexokinase (EC 2.7.1.1) | protein | 902 | 46% helix, 18% strand | P05708 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, B
- G6P · 6-O-phosphono-alpha-D-glucopyranose · sugar · 4 copies · chains A, B
- CA · Calcium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 733 | 0.77 | 0.82 | 78 | G6P |
| 2 | 1121 | 0.76 | 0.79 | 125 | BGC, G6P |
| 3 | 159 | 0.64 | 0.86 | 35 | BGC, G6P |
| 4 | 158 | 0.62 | 0.85 | 36 | BGC, G6P |
| 5 | 334 | 0.57 | 0.76 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 1883 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 1BG3 · Rat brain hexokinase type I complex with glucose and inhibitor glucose-6-phosphate · the same entry in another collection · chain A against A, TM-score 1.00
- P05708 · AlphaFold monomer V2.0 prediction for hexokinase-1 (P05708) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P05708
- Elsewhere: RCSB PDB 1BG3 · PDBe 1BG3 · UniProt P05708
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