Research workbench
Structure of polyphosphate kinase from meiothermus ruber N121D bound to ATP
Analyse Structure of polyphosphate kinase from meiothermus ruber N121D bound to ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O6M
- Type
- protein
- Length
- 1,042 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- POLYPHOSPHATE:AMP phosphotransferase
- UniProt
- A0A0S7ASE9
- Ligands
- ATP, PO4
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | POLYPHOSPHATE:AMP phosphotransferase | protein | 256 | 52% helix, 13% strand | A0A0S7ASE9 |
| B | POLYPHOSPHATE:AMP phosphotransferase | protein | 261 | 49% helix, 13% strand | A0A0S7ASE9 |
| C | POLYPHOSPHATE:AMP phosphotransferase | protein | 261 | 48% helix, 13% strand | A0A0S7ASE9 |
| D | POLYPHOSPHATE:AMP phosphotransferase | protein | 264 | 48% helix, 13% strand | A0A0S7ASE9 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 22 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 686 | 0.81 | 0.85 | 86 | PO4 |
| 2 | 280 | 0.69 | 0.84 | 45 | ATP, PO4 |
| 3 | 300 | 0.64 | 0.81 | 35 | ATP, PO4 |
| 4 | 167 | 0.60 | 0.83 | 40 | ATP, PO4 |
| 5 | 81 | 0.57 | 0.88 | 21 | ATP |
Interfaces
6 interfaces between chains.
- B–D · 1637 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 1350 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1337 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1275 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 116 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5O6M · Structure of Polyphosphate Kinase from Meiothermus ruber N121D bound to 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 A0A0S7ASE9
- Elsewhere: RCSB PDB 5O6M · PDBe 5O6M · UniProt A0A0S7ASE9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.