Research workbench
Crystal structure of thermococcus litoralis ADP-dependent glucokinase (gk)
Analyse Crystal structure of thermococcus litoralis ADP-dependent glucokinase (gk) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4B8S
- Type
- protein
- Length
- 466 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-dependent glucokinase
- EC
- 2.7.1.147
- UniProt
- Q7M537
- Ligands
- AMP, GLC
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-dependent glucokinase (EC 2.7.1.147) | protein | 466 | 48% helix, 20% strand | Q7M537 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · chains A
- GOL · Glycerol · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1054 | 0.78 | 0.80 | 74 | GLC, GOL, AMP |
| 2 | 84 | 0.58 | 0.87 | 19 | empty |
| 3 | 59 | 0.33 | 0.77 | 14 | empty |
Compared structures
- 4B8S · Crystal Structure of Thermococcus litoralis ADP-dependent Glucokinase (GK) · the same entry in another collection · chain A against A, TM-score 1.00
- Q7M537 · AlphaFold monomer V2.0 prediction for ADP-dependent GLUCOSE/GLUCOSAMINE kinase (Q7M537) · 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 Q7M537
- Elsewhere: RCSB PDB 4B8S · PDBe 4B8S · UniProt Q7M537
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