MolNFT v1 · #119009 · protein
Structure of the P2 polymerase inside in vitro assembled bacteriophage PHI6 polymerase complex, with P1 included
5FJ7 · Major inner protein P1: “Structure of the P2 polymerase inside in vitro assembled bacteriophage PHI6 polymerase complex, with P1…”. Electron microscopy, 1 ligand (MN), 20 pockets (best druggability 0.88). MolNFT v1 #119009 on…
- 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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