Research workbench
Cryo-EM structure of the human parainfluenza virus hPIV3 L-P polymerase in monomeric form
Analyse Cryo-EM structure of the human parainfluenza virus hPIV3 L-P polymerase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8KDC
- Type
- protein
- Length
- 2,329 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.3
- Source
- Human respirovirus 3
- Molecule
- RNA-directed RNA polymerase L; Phosphoprotein
- UniProt
- O89238, O89234
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · resolution 3.3 · 6 distinct chains · 53% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase L | protein | 2114 | 50% helix, 9% strand | O89238 |
| B | Phosphoprotein | protein | 65 | 65% helix, 3% strand | O89234 |
| C | Phosphoprotein | protein | 37 | 89% helix, 0% strand | O89234 |
| D | Phosphoprotein | protein | 41 | 66% helix, 7% strand | O89234 |
| E | Phosphoprotein | protein | 38 | 89% helix, 0% strand | O89234 |
| F | Phosphoprotein | protein | 34 | 82% helix, 0% strand | O89234 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 974 | 0.85 | 0.86 | 86 | empty |
| 2 | 710 | 0.82 | 0.86 | 72 | empty |
| 3 | 159 | 0.77 | 0.94 | 31 | empty |
| 4 | 437 | 0.75 | 0.84 | 69 | empty |
| 5 | 602 | 0.74 | 0.81 | 44 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1160 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 960 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 860 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 810 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 799 Ų buried · 7 hydrogen bonds · protein-protein
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 O89238
- Every structure of UniProt O89234
- Elsewhere: RCSB PDB 8KDC · PDBe 8KDC · UniProt O89238 · UniProt O89234
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