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
- 5O5Z
- Type
- protein
- Length
- 903 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-dependent GLUCOKINASE,ADP-dependent GLUCOKINASE,ADP- dependent glucokinase
- EC
- 2.7.1.147
- UniProt
- Q7M537
- Ligands
- AT4, GLC, SO4
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-dependent GLUCOKINASE,ADP-dependent GLUCOKINASE,ADP- dependent glucokinase (EC 2.7.1.147) | protein | 454 | 49% helix, 20% strand | Q7M537 |
| B | ADP-dependent GLUCOKINASE,ADP-dependent GLUCOKINASE,ADP- dependent glucokinase (EC 2.7.1.147) | protein | 449 | 49% helix, 20% strand | Q7M537 |
Ligands and binding sites
- AT4 · 5'-O-[(R)-hydroxy(thiophosphonooxy)phosphoryl]adenosine · ligand · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · chains B
- SO4 · Sulfate ion · ion · chains A, B
- GOL · Glycerol · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1109 | 0.77 | 0.79 | 95 | SO4, AT4, GOL |
| 2 | 1045 | 0.77 | 0.79 | 69 | GLC, AT4 |
| 3 | 637 | 0.66 | 0.76 | 68 | GOL |
| 4 | 85 | 0.55 | 0.86 | 17 | empty |
| 5 | 152 | 0.43 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 939 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5O5Z · 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 B against A, TM-score 0.90
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 5O5Z · PDBe 5O5Z · UniProt Q7M537
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