MolNFT v1 · #124304 · protein
High-resolution structure of the adenosine kinase from mus musculus in complex with adenosine
5KB6: “High-resolution structure of the adenosine kinase from mus musculus in complex with adenosine”. X-ray diffraction, 3 ligands (ADN, SO4, CL), 9 pockets (best druggability 0.73). MolNFT v1 #124304 on GenesisL1: 3D structure, binding…
- PDB
- 5KB6
- Type
- protein
- Length
- 686 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosine kinase
- EC
- 2.7.1.20
- UniProt
- P55264
- Ligands
- ADN, SO4, CL
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Adenosine kinase (EC 2.7.1.20) | protein | 343 | 41% helix, 23% strand | P55264 |
Ligands and binding sites
- ADN · Adenosine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 3 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 645 | 0.73 | 0.80 | 74 | ADN, CL, ACT |
| 2 | 631 | 0.71 | 0.79 | 75 | ADN, CL, ACT |
| 3 | 213 | 0.50 | 0.76 | 27 | empty |
| 4 | 134 | 0.45 | 0.77 | 21 | SO4 |
| 5 | 133 | 0.44 | 0.77 | 21 | SO4 |
Interfaces
1 interface between chains.
- A–B · 601 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5KB6 · High-resolution structure of the adenosine kinase from Mus musculus in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P55264 · AlphaFold monomer V2.0 prediction for adenosine kinase (P55264) · a predicted model of the same protein · chain B against A, TM-score 0.89
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 P55264
- Elsewhere: RCSB PDB 5KB6 · PDBe 5KB6 · UniProt P55264
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