MolNFT v1 · #125852 · protein
Structure of polyphosphate kinase 2 mutant D117N from francisella tularensis with polyphosphate
5LLF: “Structure of polyphosphate kinase 2 mutant D117N from francisella tularensis with polyphosphate”. X-ray diffraction, 5 ligands (6YX, 6YY, 6YW), 9 pockets (best druggability 0.83). MolNFT v1 #125852 on GenesisL1: 3D structure…
- PDB
- 5LLF
- Type
- protein
- Length
- 1,058 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
- 6YX, 6YY, 6YW, PO4, CL
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Polyphosphate kinase 2 (EC 2.7.4.1) | protein | 264 | 50% helix, 14% strand | Q5NEQ5 |
| D | Polyphosphate kinase 2 (EC 2.7.4.1) | protein | 266 | 49% helix, 14% strand | Q5NEQ5 |
Ligands and binding sites
- 6YX · [oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phospho · ligand · chains A, B
- 6YY · bis[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl] hydrogen phosphate · ligand · chains C
- 6YW · [oxidanyl-[oxidanyl-[oxidanyl(phosphonooxy) phosphoryl]oxy-phosphoryl]oxy-phosphoryl] phosphono hydrogen phosphate · ligand · chains D
- PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1106 | 0.83 | 0.84 | 118 | 6YW |
| 2 | 567 | 0.79 | 0.85 | 69 | 6YY |
| 3 | 571 | 0.79 | 0.85 | 72 | empty |
| 4 | 50 | 0.59 | 0.92 | 19 | empty |
| 5 | 104 | 0.38 | 0.75 | 20 | empty |
Interfaces
4 interfaces between chains.
- B–D · 790 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 754 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 318 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 283 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5LLF · Structure of Polyphosphate Kinase 2 mutant D117N from Francisella tularensis 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 Q5NEQ5
- Elsewhere: RCSB PDB 5LLF · PDBe 5LLF · UniProt Q5NEQ5
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