MolNFT v1 · #124303 · protein
Crystal structure of the adenosine kinase from mus musculus in complex with adenosine and adenosine-diphosphate
5KB5: “Crystal structure of the adenosine kinase from mus musculus in complex with adenosine and…”. X-ray diffraction, 6 ligands (ADN, ADP, MG), 3 pockets (best druggability 0.78). MolNFT v1 #124303 on GenesisL1: 3D structure, binding…
- PDB
- 5KB5
- Type
- protein
- Length
- 341 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosine kinase
- EC
- 2.7.1.20
- UniProt
- P55264
- Ligands
- ADN, ADP, MG, K, PO4, CL
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosine kinase (EC 2.7.1.20) | protein | 341 | 43% helix, 24% strand | P55264 |
Ligands and binding sites
- ADN · Adenosine · ligand · chains A
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- K · Potassium ion · metal · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A
- CL · Chloride ion · ion · chains A
- PG4 · Tetraethylene glycol · additive · 2 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 410 | 0.78 | 0.87 | 63 | ADN, ADP, CL, MG |
| 2 | 135 | 0.46 | 0.78 | 18 | PO4 |
| 3 | 123 | 0.42 | 0.75 | 22 | empty |
Compared structures
- 5KB5 · Crystal structure of the adenosine kinase from Mus musculus in complex with adenosine and… · 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 A against A, TM-score 0.99
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 5KB5 · PDBe 5KB5 · UniProt P55264
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