MolNFT v2 · #145858 · protein
Mycobacterium tuberculosis adenosine kinase bound to sangivamycin
6C9N: “Mycobacterium tuberculosis adenosine kinase bound to sangivamycin”. X-ray diffraction at 2.1, 3 ligands (SGV, NA, SO4), 2 pockets (best druggability 0.77). MolNFT v2 #145858 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6C9N
- Type
- protein
- Length
- 625 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Mycobacterium tuberculosis
- Molecule
- Adenosine kinase
- EC
- 2.7.1.20
- UniProt
- A5U4N0
- Ligands
- SGV, NA, SO4
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · resolution 2.1 · 2 distinct chains · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosine kinase (EC 2.7.1.20) | protein | 311 | 43% helix, 23% strand | A5U4N0 |
| B | Adenosine kinase (EC 2.7.1.20) | protein | 314 | 44% helix, 23% strand | A5U4N0 |
Ligands and binding sites
- SGV · Sangivamycin · ligand · 4 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 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
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 | 675 | 0.77 | 0.82 | 64 | SGV, SO4 |
| 2 | 636 | 0.77 | 0.82 | 64 | SGV, SO4 |
Interfaces
1 interface between chains.
- A–B · 1161 Ų buried · 17 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 6C9N · PDBe 6C9N · UniProt A5U4N0
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