MolNFT v1 · #127295 · protein + RNA
Influenza B polymerase bound to vrna promoter and capped RNA primer
5MSG · Polymerase acidic protein: “Influenza B polymerase bound to vrna promoter and capped RNA primer”. X-ray diffraction, 2 ligands (M7G, PO4), 20 pockets (best druggability 0.89). MolNFT v1 #127295 on GenesisL1: 3D structure, binding…
- PDB
- 5MSG
- Type
- protein + RNA
- Length
- 2,229 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polymerase acidic protein; RNA-directed RNA polymerase catalytic subunit; Polymerase…
- EC
- 2.7.7.48
- UniProt
- Q5V8Z9, Q5V8Y6, Q5V8X3
- Ligands
- M7G, PO4
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 6 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase acidic protein | protein | 717 | 46% helix, 16% strand | Q5V8Z9 |
| B | RNA-directed RNA polymerase catalytic subunit (EC 2.7.7.48) | protein | 746 | 47% helix, 17% strand | Q5V8Y6 |
| C | Polymerase basic protein 2 | protein | 731 | 37% helix, 20% strand | Q5V8X3 |
| M | RNA (5'-D(*(GDM))-R(P*AP*AP*UP*C)-3') | rna | 4 | — | — |
| R | RNA (5'- R(*UP*AP*UP*AP*CP*CP*UP*CP*UP*GP*CP*UP*UP*CP*UP*GP*CP*U)-3') | rna | 17 | — | — |
| V | RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*AP*G)-3') | rna | 14 | — | — |
Ligands and binding sites
- M7G · 7N-methyl-8-hydroguanosine-5'-diphosphate · ligand · chains C, M
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
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 | 992 | 0.89 | 0.91 | 115 | empty |
| 2 | 1134 | 0.84 | 0.85 | 103 | empty |
| 3 | 366 | 0.80 | 0.90 | 37 | M7G |
| 4 | 929 | 0.78 | 0.81 | 72 | empty |
| 5 | 341 | 0.78 | 0.88 | 55 | empty |
Interfaces
10 interfaces between chains.
- A–B · 9086 Ų buried · 141 hydrogen bonds · protein-protein
- B–C · 7192 Ų buried · 82 hydrogen bonds · protein-protein
- A–C · 2226 Ų buried · 21 hydrogen bonds · protein-protein
- A–V · 1249 Ų buried · 22 hydrogen bonds · protein-nucleic
- B–R · 1161 Ų buried · 24 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5MSG · Influenza B polymerase bound to vRNA promoter and capped RNA primer · 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 Q5V8Z9
- Every structure of UniProt Q5V8Y6
- Every structure of UniProt Q5V8X3
- Elsewhere: RCSB PDB 5MSG · PDBe 5MSG · UniProt Q5V8Z9 · UniProt Q5V8Y6 · UniProt Q5V8X3
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