MolNFT v1 · #55365 · protein
Structure of the RNA polymerase VP1 from infectious pancreatic necrosis virus in complex with magnesium
2YI9 · RNA-directed RNA polymerase: “Structure of the RNA polymerase VP1 from infectious pancreatic necrosis virus in complex with magnesium”. X-ray diffraction, 3 ligands (MG, K, CL), 20 pockets (best druggability 0.76). MolNFT v1 #55365…
- 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.