MolNFT v1 · #125837 · protein
Structure of polyphosphate kinase 2 from francisella tularensis schu S4 with polyphosphate
5LL0: “Structure of polyphosphate kinase 2 from francisella tularensis schu S4 with polyphosphate”. X-ray diffraction, 1 ligand (9PI), 16 pockets (best druggability 0.81). MolNFT v1 #125837 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5LL0
- Type
- protein
- Length
- 963 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyphosphate kinase 2
- EC
- 2.7.4.1
- UniProt
- Q5NEQ5
- Ligands
- 9PI
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Polyphosphate kinase 2 (EC 2.7.4.1) | protein | 241 | 54% helix, 15% strand | Q5NEQ5 |
| C | Polyphosphate kinase 2 (EC 2.7.4.1) | protein | 239 | 50% helix, 14% strand | Q5NEQ5 |
| D | Polyphosphate kinase 2 (EC 2.7.4.1) | protein | 242 | 49% helix, 14% strand | Q5NEQ5 |
Ligands and binding sites
- 9PI · Bis[oxidanyl-[oxidanyl-[oxidanyl(phosphonooxy) phosphoryl]oxy-phosphoryl]oxy-phosphoryl] hydrogen phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 770 | 0.81 | 0.84 | 101 | 9PI |
| 2 | 358 | 0.73 | 0.85 | 57 | 9PI |
| 3 | 363 | 0.70 | 0.83 | 58 | 9PI |
| 4 | 83 | 0.68 | 0.93 | 20 | empty |
| 5 | 209 | 0.64 | 0.83 | 31 | 9PI |
Interfaces
4 interfaces between chains.
- A–C · 1126 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 1099 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 798 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 708 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5LL0 · Structure of Polyphosphate Kinase 2 from Francisella tularensis SCHU S4 with polyphosphate · 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 Q5NEQ5
- Elsewhere: RCSB PDB 5LL0 · PDBe 5LL0 · UniProt Q5NEQ5
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