Research workbench
Adenosine kinase from schistosoma mansoni in complex with 2- fluoroadenosine
Analyse Adenosine kinase from schistosoma mansoni in complex with 2- fluoroadenosine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DC3
- Type
- protein
- Length
- 683 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosine kinase
- EC
- 2.7.1.20
- UniProt
- G4V7G8
- Ligands
- ADN, 2FA, CL
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosine kinase (EC 2.7.1.20) | protein | 339 | 43% helix, 22% strand | G4V7G8 |
| B | Adenosine kinase (EC 2.7.1.20) | protein | 344 | 41% helix, 22% strand | G4V7G8 |
Ligands and binding sites
- ADN · Adenosine · ligand · chains A
- 2FA · 2-(6-amino-2-fluoro-purin-9-yl)-5-hydroxymethyl-tetrahydro-furan-3,4-diol · ligand · chains B
- CL · Chloride ion · ion · 2 copies · chains A, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 605 | 0.78 | 0.84 | 62 | 2FA, CL |
| 2 | 416 | 0.78 | 0.87 | 58 | ADN, CL |
| 3 | 350 | 0.56 | 0.75 | 44 | empty |
| 4 | 274 | 0.54 | 0.75 | 41 | empty |
| 5 | 231 | 0.51 | 0.76 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 658 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4DC3 · Adenosine kinase from Schistosoma mansoni in complex with 2-fluoroadenosine · 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 G4V7G8
- Elsewhere: RCSB PDB 4DC3 · PDBe 4DC3 · UniProt G4V7G8
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