Research workbench
Crystal structure of sulfolobus tokodaii hexokinase in complex with ADP
Analyse Crystal structure of sulfolobus tokodaii hexokinase in complex with ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2E2P
- Type
- protein
- Length
- 595 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hexokinase
- EC
- 2.7.1.1
- UniProt
- Q96Y14
- Ligands
- ADP, SO4
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hexokinase (EC 2.7.1.1) | protein | 298 | 51% helix, 19% strand | Q96Y14 |
| B | Hexokinase (EC 2.7.1.1) | protein | 297 | 51% helix, 19% strand | Q96Y14 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 546 | 0.66 | 0.77 | 47 | empty |
| 2 | 523 | 0.65 | 0.77 | 43 | empty |
| 3 | 293 | 0.56 | 0.76 | 25 | SO4 |
| 4 | 102 | 0.35 | 0.74 | 22 | empty |
| 5 | 86 | 0.33 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1908 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 2E2P · Crystal structure of Sulfolobus tokodaii hexokinase in complex with 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 2E2P · PDBe 2E2P · UniProt Q96Y14
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.