Research workbench
Structure of the P2 polymerase inside in vitro assembled bacteriophage PHI6 polymerase complex, with P1 included
Analyse Structure of the P2 polymerase inside in vitro assembled bacteriophage PHI6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FJ7
- Type
- protein
- Length
- 2,186 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major inner protein P1; RNA-directed RNA polymerase
- UniProt
- P11126, P11124
- Ligands
- MN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 2 distinct chains · 42% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Major inner protein P1 | protein | 761 | 42% helix, 3% strand | P11126 |
| C | RNA-directed RNA polymerase | protein | 664 | 42% helix, 10% strand | P11124 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1153 | 0.88 | 0.89 | 135 | empty |
| 2 | 840 | 0.86 | 0.88 | 117 | empty |
| 3 | 836 | 0.86 | 0.88 | 100 | empty |
| 4 | 125 | 0.80 | 0.97 | 34 | empty |
| 5 | 168 | 0.77 | 0.93 | 40 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1253 Ų buried · 63 hydrogen bonds · protein-protein
- A–C · 157 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5FJ7 · Structure of the P2 polymerase inside in vitro assembled bacteriophage phi6 polymerase… · 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 P11126
- Every structure of UniProt P11124
- Elsewhere: RCSB PDB 5FJ7 · PDBe 5FJ7 · UniProt P11126 · UniProt P11124
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