Research workbench
Crystal structure of dimeric KLHXK1 in crystal form VII with glucose bound (open state)
Analyse Crystal structure of dimeric KLHXK1 in crystal form VII with glucose bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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