MolNFT v1 · #139152 · protein
Crystal structure of adenylate kinase
5X6K · Adenylate kinase isoenzyme 1: “Crystal structure of adenylate kinase”. X-ray diffraction, 2 ligands (AP5, SO4), 4 pockets (best druggability 0.75). MolNFT v1 #139152 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5X6K
- Type
- protein
- Length
- 370 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylate kinase isoenzyme 1
- Ligands
- AP5, SO4
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 59% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Adenylate kinase isoenzyme 1 | protein | 185 | 59% helix, 14% strand | — |
Ligands and binding sites
- AP5 · Bis(adenosine)-5'-pentaphosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
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 | 326 | 0.75 | 0.87 | 44 | AP5 |
| 2 | 365 | 0.75 | 0.86 | 49 | AP5 |
| 3 | 135 | 0.39 | 0.73 | 17 | empty |
| 4 | 50 | 0.25 | 0.73 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 301 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5X6K · Crystal structure of adenylate kinase · 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
- Elsewhere: RCSB PDB 5X6K · PDBe 5X6K
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