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Characterisation of polyphosphate kinase 2 from the intracellular pathogen francisella tularensis
Analyse Characterisation of polyphosphate kinase 2 from the intracellular pathogen… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YEG
- Type
- protein
- Length
- 1,030 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
- A0A080S703
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyphosphate kinase 2 (EC 2.7.4.1) | protein | 266 | 53% helix, 14% strand | A0A080S703 |
| B | Polyphosphate kinase 2 (EC 2.7.4.1) | protein | 258 | 47% helix, 14% strand | A0A080S703 |
| C | Polyphosphate kinase 2 (EC 2.7.4.1) | protein | 251 | 47% helix, 14% strand | A0A080S703 |
| D | Polyphosphate kinase 2 (EC 2.7.4.1) | protein | 255 | 46% helix, 14% strand | A0A080S703 |
Pockets
13 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 198 | 0.82 | 0.96 | 30 | empty |
| 2 | 324 | 0.78 | 0.89 | 44 | empty |
| 3 | 66 | 0.73 | 0.97 | 17 | empty |
| 4 | 417 | 0.71 | 0.82 | 62 | empty |
| 5 | 457 | 0.71 | 0.81 | 62 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1095 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1080 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 500 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 24 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4YEG · Characterisation of Polyphosphate Kinase 2 from the Intracellular Pathogen Francisella… · 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 A0A080S703
- Elsewhere: RCSB PDB 4YEG · PDBe 4YEG · UniProt A0A080S703
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