Research workbench
Mycobacterium tuberculosis adenosine kinase bound to (2R,3S,4R,5R)-2- (hydroxymethyl)-5-(6-(thiophen-3-yl)-9H-purin-9-YL)TETRAHYDROFURAN-3, 4-diol
Analyse Mycobacterium tuberculosis adenosine kinase bound to (2R,3S,4R,5R)-2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C9R
- Type
- protein
- Length
- 674 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosine kinase
- EC
- 2.7.1.20
- UniProt
- A5U4N0
- Ligands
- ERJ, NA
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Adenosine kinase (EC 2.7.1.20) | protein | 337 | 45% helix, 22% strand | A5U4N0 |
Ligands and binding sites
- ERJ · 9-beta-D-ribofuranosyl-6-(thiophen-3-yl)-9H-purine · ligand · 4 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 977 | 0.78 | 0.80 | 81 | ERJ |
| 2 | 901 | 0.77 | 0.80 | 74 | ERJ |
| 3 | 51 | 0.33 | 0.78 | 16 | empty |
| 4 | 50 | 0.27 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1487 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
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 A5U4N0
- Elsewhere: RCSB PDB 6C9R · PDBe 6C9R · UniProt A5U4N0
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