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Crystal structure of Sulfolobus tokodaii hexokinase in complex with xylose, Mg2+, and ADP
Analyse Crystal structure of Sulfolobus tokodaii hexokinase in complex with xylose… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2E2Q
- Type
- protein
- Length
- 593 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Sulfolobus tokodaii
- Molecule
- Hexokinase
- EC
- 2.7.1.1
- UniProt
- Q96Y14
- Ligands
- ADP, XYP, MG
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · resolution 2 · 2 distinct chains · 51% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hexokinase (EC 2.7.1.1) | protein | 297 | 52% helix, 19% strand | Q96Y14 |
| B | Hexokinase (EC 2.7.1.1) | protein | 296 | 50% helix, 19% strand | Q96Y14 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- XYP · beta-D-xylopyranose · sugar · chains A, B
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 368 | 0.70 | 0.83 | 53 | XYP, MG, ADP |
| 2 | 601 | 0.68 | 0.77 | 49 | empty |
| 3 | 256 | 0.55 | 0.77 | 35 | empty |
| 4 | 71 | 0.32 | 0.75 | 19 | empty |
| 5 | 52 | 0.27 | 0.75 | 12 | ADP |
Interfaces
1 interface between chains.
- A–B · 1894 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 2E2Q · Crystal structure of sulfolobus tokodaii hexokinase in complex with xylose, MG2+, and ADP · the same entry in another collection · chain A against A, TM-score 1.00
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 Q96Y14
- Elsewhere: RCSB PDB 2E2Q · PDBe 2E2Q · UniProt Q96Y14
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