MolNFT v1 · #100530 · protein
Structure of trypanosoma brucei brucei adenosine kinase in complex with adenosine and amppnp
4N09: “Structure of trypanosoma brucei brucei adenosine kinase in complex with adenosine and amppnp”. X-ray diffraction, 2 ligands (ADN, ADP), 13 pockets (best druggability 0.81). MolNFT v1 #100530 on GenesisL1: 3D structure, binding sites…
- PDB
- 4N09
- Type
- protein
- Length
- 1,377 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosine kinase
- EC
- 2.7.1.20
- UniProt
- Q584S0
- Ligands
- ADN, ADP
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Adenosine kinase (EC 2.7.1.20) | protein | 345 | 43% helix, 22% strand | Q584S0 |
| D | Adenosine kinase (EC 2.7.1.20) | protein | 342 | 43% helix, 23% strand | Q584S0 |
Ligands and binding sites
- ADN · Adenosine · ligand · 4 copies · chains A, B, C, D
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 623 | 0.81 | 0.86 | 75 | ADN, ADP |
| 2 | 584 | 0.79 | 0.85 | 63 | ADN, ADP, EDO |
| 3 | 670 | 0.79 | 0.84 | 76 | ADN, ADP, EDO |
| 4 | 612 | 0.76 | 0.82 | 77 | ADN, ADP |
| 5 | 515 | 0.75 | 0.83 | 69 | empty |
Interfaces
3 interfaces between chains.
- A–B · 951 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 676 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 635 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4N09 · Structure of Trypanosoma brucei brucei adenosine kinase in complex with adenosine and… · 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 Q584S0
- Elsewhere: RCSB PDB 4N09 · PDBe 4N09 · UniProt Q584S0
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