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Structure of the RNA polymerase VP1 from infectious pancreatic necrosis virus in complex with magnesium
Analyse Structure of the RNA polymerase VP1 from infectious pancreatic necrosis virus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YI9
- Type
- protein
- Length
- 3,855 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase
- EC
- 2.7.7.48, 2.7.7.49
- UniProt
- P22173
- Ligands
- MG, K, CL
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | RNA-directed RNA polymerase (EC 2.7.7.48, 2.7.7.49) | protein | 771 | 47% helix, 14% strand | P22173 |
Ligands and binding sites
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, E
- K · Potassium ion · metal · 5 copies · chains A, B, C, D, E
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E
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 | 919 | 0.76 | 0.79 | 120 | empty |
| 2 | 784 | 0.74 | 0.79 | 93 | empty |
| 3 | 288 | 0.71 | 0.85 | 35 | empty |
| 4 | 907 | 0.70 | 0.75 | 95 | MG, CL |
| 5 | 783 | 0.69 | 0.75 | 74 | MG, CL |
Interfaces
7 interfaces between chains.
- A–C · 1068 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 1060 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 1059 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 1056 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 447 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2YI9 · Structure of the RNA polymerase VP1 from Infectious Pancreatic Necrosis Virus in 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 P22173
- Elsewhere: RCSB PDB 2YI9 · PDBe 2YI9 · UniProt P22173
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