Research workbench
Crystal structure of polyphosphate kinase 2 from deinococcus radiodurans in complex with ADP
Analyse Crystal structure of polyphosphate kinase 2 from deinococcus radiodurans in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NMJ
- Type
- protein
- Length
- 1,064 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PPK2 domain-containing protein
- UniProt
- Q9RY20
- Ligands
- ADP, MG, PO4
- Pockets
- 14 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | PPK2 domain-containing protein | protein | 266 | 54% helix, 12% strand | Q9RY20 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D
- MG · Magnesium ion · metal · chains D
- PO4 · Phosphate ion · ion · chains D
- GOL · Glycerol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 346 | 0.74 | 0.86 | 52 | empty |
| 2 | 414 | 0.69 | 0.81 | 59 | ADP |
| 3 | 195 | 0.68 | 0.86 | 30 | empty |
| 4 | 201 | 0.64 | 0.84 | 32 | PO4 |
| 5 | 205 | 0.63 | 0.83 | 33 | GOL |
Interfaces
6 interfaces between chains.
- B–C · 1580 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 1557 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 1039 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1027 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 57 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7NMJ · Crystal structure of Polyphosphate Kinase 2 from Deinococcus radiodurans in complex with… · 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 7NMJ · PDBe 7NMJ · UniProt Q9RY20
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.