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Crystal structure of trypanosoma brucei rhodesiense adenosine kinase complexed with inhibitor AP5A
Analyse Crystal structure of trypanosoma brucei rhodesiense adenosine kinase complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OTX
- Type
- protein
- Length
- 680 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosine kinase, putative
- EC
- 2.7.1.20
- UniProt
- Q584S0
- Ligands
- AP5, NA
- Pockets
- 2 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosine kinase, putative (EC 2.7.1.20) | protein | 338 | 43% helix, 23% strand | Q584S0 |
| B | Adenosine kinase, putative (EC 2.7.1.20) | protein | 342 | 42% helix, 24% strand | Q584S0 |
Ligands and binding sites
- AP5 · Bis(adenosine)-5'-pentaphosphate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 874 | 0.85 | 0.87 | 101 | AP5, NA |
| 2 | 777 | 0.82 | 0.85 | 94 | AP5, NA |
Interfaces
1 interface between chains.
- A–B · 493 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3OTX · Crystal Structure of Trypanosoma brucei rhodesiense Adenosine Kinase Complexed with… · 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 3OTX · PDBe 3OTX · UniProt Q584S0
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