Research workbench
Crystal structure of polyphosphate kinase from meiothermus ruber bound to ADP
Analyse Crystal structure of polyphosphate kinase from meiothermus ruber bound to ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LDB
- Type
- protein
- Length
- 1,039 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- POLYPHOSPHATE:AMP phosphotransferase
- UniProt
- A0A0S7ASE9
- Ligands
- ADP, MG, PO4, CL
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | POLYPHOSPHATE:AMP phosphotransferase | protein | 258 | 50% helix, 13% strand | A0A0S7ASE9 |
| B, D | POLYPHOSPHATE:AMP phosphotransferase | protein | 260 | 50% helix, 13% strand | A0A0S7ASE9 |
| C | POLYPHOSPHATE:AMP phosphotransferase | protein | 261 | 47% helix, 13% strand | A0A0S7ASE9 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 777 | 0.82 | 0.85 | 88 | MG |
| 2 | 204 | 0.61 | 0.82 | 31 | PO4, MG, GOL |
| 3 | 116 | 0.58 | 0.85 | 31 | ADP |
| 4 | 162 | 0.58 | 0.82 | 34 | ADP |
| 5 | 109 | 0.57 | 0.85 | 28 | PO4, MG |
Interfaces
6 interfaces between chains.
- B–C · 1580 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 1418 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1373 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1357 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 139 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5LDB · Crystal Structure of Polyphosphate Kinase from Meiothermus ruber bound to ADP · 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 5LDB · PDBe 5LDB · UniProt A0A0S7ASE9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.