Research workbench
Structure of Polyphosphate Kinase from Meiothermus ruber bound to AMP
Analyse Structure of Polyphosphate Kinase from Meiothermus ruber bound to AMP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LCD
- Type
- protein
- Length
- 1,028 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.66
- Source
- Meiothermus ruber H328
- Molecule
- Polyphosphate:AMP phosphotransferase
- UniProt
- A0A0S7ASE9
- Ligands
- AMP, MG, SO4, PO4
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · resolution 2.66 · 2 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Polyphosphate:AMP phosphotransferase | protein | 256 | 50% helix, 13% strand | A0A0S7ASE9 |
| B, D | Polyphosphate:AMP phosphotransferase | protein | 258 | 49% helix, 13% strand | A0A0S7ASE9 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · chains C
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 597 | 0.80 | 0.86 | 90 | SO4 |
| 2 | 318 | 0.70 | 0.84 | 51 | AMP, MG, PO4, SO4 |
| 3 | 205 | 0.62 | 0.83 | 31 | PO4 |
| 4 | 138 | 0.60 | 0.84 | 32 | AMP |
| 5 | 150 | 0.57 | 0.82 | 26 | PO4, SO4 |
Interfaces
6 interfaces between chains.
- A–B · 1314 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1314 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1111 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 1108 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 144 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5LCD · Structure of polyphosphate kinase from meiothermus ruber bound to AMP · 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 5LCD · PDBe 5LCD · UniProt A0A0S7ASE9
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