MolNFT v1 · #73550 · protein
Crystal structure of dimeric KLHXK1 in crystal form VII with glucose bound (open state)
3O5B · Hexokinase: “Crystal structure of dimeric KLHXK1 in crystal form VII with glucose bound (open state)”. X-ray diffraction, 2 ligands (BGC, SO4), 7 pockets (best druggability 0.65). MolNFT v1 #73550 on GenesisL1: 3D structure, binding…
- PDB
- 3O5B
- Type
- protein
- Length
- 957 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hexokinase
- EC
- 2.7.1.1
- UniProt
- P33284
- Ligands
- BGC, SO4
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hexokinase (EC 2.7.1.1) | protein | 479 | 44% helix, 17% strand | P33284 |
| B | Hexokinase (EC 2.7.1.1) | protein | 478 | 45% helix, 18% strand | P33284 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 632 | 0.65 | 0.75 | 73 | BGC, SO4 |
| 2 | 519 | 0.61 | 0.75 | 64 | BGC, SO4 |
| 3 | 108 | 0.40 | 0.76 | 25 | empty |
| 4 | 81 | 0.33 | 0.75 | 18 | empty |
| 5 | 96 | 0.32 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1162 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3O5B · Crystal structure of dimeric KlHxk1 in crystal form VII with glucose bound (open state) · the same entry in another collection · chain A against A, TM-score 1.00
- P33284 · AlphaFold monomer V2.0 prediction for hexokinase (P33284) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P33284
- Elsewhere: RCSB PDB 3O5B · PDBe 3O5B · UniProt P33284
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