MolNFT v1 · #39827 · protein
Human adenosine kinase in complex with 5'-deoxy-5-iodotubercidin
2I6A: “Human adenosine kinase in complex with 5'-deoxy-5-iodotubercidin”. X-ray diffraction, 1 ligand (5I5), 20 pockets (best druggability 0.83). MolNFT v1 #39827 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2I6A
- Type
- protein
- Length
- 1,372 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosine kinase
- UniProt
- Q5VXR3
- Ligands
- 5I5
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Adenosine kinase | protein | 343 | 42% helix, 23% strand | Q5VXR3 |
Ligands and binding sites
- 5I5 · 7-(5-deoxy-beta-D-ribofuranosyl)-5-iodo-7H-pyrrolo[2,3-d]pyrimidin-4-amine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 506 | 0.83 | 0.90 | 84 | 5I5 |
| 2 | 563 | 0.83 | 0.89 | 89 | 5I5 |
| 3 | 461 | 0.83 | 0.90 | 78 | 5I5 |
| 4 | 510 | 0.82 | 0.89 | 82 | 5I5 |
| 5 | 297 | 0.68 | 0.83 | 38 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1159 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1098 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 255 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 228 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2I6A · Human Adenosine Kinase in Complex With 5'-Deoxy-5-Iodotubercidin · 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 Q5VXR3
- Elsewhere: RCSB PDB 2I6A · PDBe 2I6A · UniProt Q5VXR3
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