Research workbench
Crystal structure of polyphosphate kinase from porphyromonas gingivalis
Analyse Crystal structure of polyphosphate kinase from porphyromonas gingivalis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2O8R
- Type
- protein
- Length
- 1,253 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyphosphate kinase
- EC
- 2.7.4.1
- UniProt
- Q7MTR1
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyphosphate kinase (EC 2.7.4.1) | protein | 648 | 38% helix, 21% strand | Q7MTR1 |
| B | Polyphosphate kinase (EC 2.7.4.1) | protein | 605 | 38% helix, 21% strand | Q7MTR1 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 13 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.74 | 0.98 | 21 | SO4 |
| 2 | 428 | 0.74 | 0.83 | 56 | empty |
| 3 | 56 | 0.73 | 0.99 | 18 | empty |
| 4 | 803 | 0.73 | 0.78 | 76 | SO4 |
| 5 | 451 | 0.72 | 0.82 | 61 | empty |
Interfaces
1 interface between chains.
- A–B · 2472 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 35 modified (engineered).
Compared structures
- 2O8R · Crystal Structure of Polyphosphate Kinase from Porphyromonas Gingivalis · 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 Q7MTR1
- Elsewhere: RCSB PDB 2O8R · PDBe 2O8R · UniProt Q7MTR1
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