Research workbench
Parainfluenza virus 5 L-P complex
Analyse Parainfluenza virus 5 L-P complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V85
- Type
- protein
- Length
- 2,240 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase L; Phosphoprotein
- EC
- 2.7.7.48, 2.1.1.56, 2.7.7.88, 2.1.1.296
- UniProt
- Q88434, P11208
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 4 distinct chains · 52% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase L (EC 2.7.7.48, 2.1.1.56, 2.7.7.88, 2.1.1.296) | protein | 1901 | 48% helix, 5% strand | Q88434 |
| F | Phosphoprotein | protein | 47 | 79% helix, 0% strand | P11208 |
| B, D | Phosphoprotein | protein | 72 | 94% helix, 1% strand | P11208 |
| C, E | Phosphoprotein | protein | 74 | 93% helix, 1% strand | P11208 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A
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 | 771 | 0.84 | 0.87 | 120 | empty |
| 2 | 211 | 0.78 | 0.92 | 36 | empty |
| 3 | 609 | 0.77 | 0.83 | 92 | empty |
| 4 | 782 | 0.75 | 0.80 | 72 | empty |
| 5 | 1068 | 0.75 | 0.77 | 103 | empty |
Interfaces
9 interfaces between chains.
- B–E · 1785 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1784 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1704 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1694 Ų buried · 17 hydrogen bonds · protein-protein
- A–F · 634 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6V85 · Parainfluenza virus 5 L-P complex · 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 Q88434
- Every structure of UniProt P11208
- Elsewhere: RCSB PDB 6V85 · PDBe 6V85 · UniProt Q88434 · UniProt P11208
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