Research workbench
Influenza a virus (A/NT/60/1968) polymerase heterotrimer bound to 3'5' vrna promoter and capped RNA primer
Analyse Influenza a virus (A/NT/60/1968) polymerase heterotrimer bound to 3'5' vrna… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RR7
- Type
- protein + RNA
- Length
- 2,227 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polymerase acidic protein; RNA-directed RNA polymerase catalytic subunit; Polymerase…
- EC
- 3.1.-.-, 2.7.7.48
- UniProt
- P03434, P03432, P03429
- Ligands
- M7G
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 6 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase acidic protein (EC 3.1.-.-) | protein | 716 | 42% helix, 16% strand | P03434 |
| B | RNA-directed RNA polymerase catalytic subunit (EC 2.7.7.48) | protein | 744 | 44% helix, 15% strand | P03432 |
| C | Polymerase basic protein 2 | protein | 737 | 33% helix, 20% strand | P03429 |
| F | RNA (5'-D(*(M7G))-R(P*AP*AP*UP*CP*U)-3') | rna | 5 | — | — |
| E | RNA (5'-R(P*GP*CP*CP*UP*GP*CP*UP*UP*UP*UP*G)-3') | rna | 11 | — | — |
| D | RNA (5'-R(P*AP*GP*UP*AP*GP*AP*AP*AP*CP*AP*AP*GP*GP*C)-3') | rna | 14 | — | — |
Ligands and binding sites
- M7G · 7N-methyl-8-hydroguanosine-5'-diphosphate · ligand · chains C, F
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 | 949 | 0.88 | 0.90 | 137 | empty |
| 2 | 767 | 0.87 | 0.91 | 102 | empty |
| 3 | 367 | 0.82 | 0.91 | 40 | M7G |
| 4 | 305 | 0.80 | 0.91 | 58 | empty |
| 5 | 791 | 0.80 | 0.83 | 60 | empty |
Interfaces
10 interfaces between chains.
- A–B · 8835 Ų buried · 97 hydrogen bonds · protein-protein
- B–C · 7707 Ų buried · 65 hydrogen bonds · protein-protein
- A–C · 1568 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 1350 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–E · 1090 Ų buried · 23 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6RR7 · Influenza A virus (A/NT/60/1968) polymerase Heterotrimer bound to 3'5' vRNA promoter and… · 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 P03434
- Every structure of UniProt P03432
- Every structure of UniProt P03429
- Elsewhere: RCSB PDB 6RR7 · PDBe 6RR7 · UniProt P03434 · UniProt P03432 · UniProt P03429
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