Research workbench
Crystal structure of PPK2 in complex with mg ATP
Analyse Crystal structure of PPK2 in complex with mg ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AQE
- Type
- protein
- Length
- 531 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Molecule a
- UniProt
- Q9RY20
- Ligands
- ATP, MG, CL
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Molecule a | protein | 265 | 55% helix, 12% strand | Q9RY20 |
| B | Molecule a | protein | 266 | 54% helix, 12% strand | Q9RY20 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · 5 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · 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 | 919 | 0.78 | 0.80 | 91 | ATP, MG, GOL |
| 2 | 554 | 0.72 | 0.80 | 54 | ATP, MG |
Interfaces
1 interface between chains.
- A–B · 1661 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 6AQE · Crystal structure of PPK2 in complex with Mg ATP · 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 Q9RY20
- Elsewhere: RCSB PDB 6AQE · PDBe 6AQE · UniProt Q9RY20
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