Research workbench
Mycobacterium tuberculosis adenosine kinase bound to iodotubercidin
Analyse Mycobacterium tuberculosis adenosine kinase bound to iodotubercidin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C67
- Type
- protein
- Length
- 627 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosine kinase
- EC
- 2.7.1.20
- UniProt
- P9WID5
- Ligands
- 5ID, NA, SO4
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosine kinase (EC 2.7.1.20) | protein | 313 | 43% helix, 23% strand | P9WID5 |
| B | Adenosine kinase (EC 2.7.1.20) | protein | 314 | 44% helix, 23% strand | P9WID5 |
Ligands and binding sites
- 5ID · (2R,3R,4S,5R)-2-(4-amino-5-iodo-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-5-(hydroxymethyl)tetrahydrofuran-3, 4-diol · 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
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 659 | 0.77 | 0.82 | 70 | 5ID, SO4 |
| 2 | 618 | 0.76 | 0.82 | 65 | 5ID, SO4 |
| 3 | 53 | 0.36 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1215 Ų buried · 16 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 P9WID5
- Elsewhere: RCSB PDB 6C67 · PDBe 6C67 · UniProt P9WID5
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