Research workbench
Crystal structure of bat influenza A/H17N10 polymerase with viral RNA promoter and capped RNA primer
Analyse Crystal structure of bat influenza A/H17N10 polymerase with viral RNA promoter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EVJ
- Type
- protein + RNA
- Length
- 4,472 residues
- Chains
- 12
- 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
- H6QM92, H6QM91, H6QM90
- Ligands
- 8NK
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 9 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase acidic protein | protein | 709 | 45% helix, 18% strand | H6QM92 |
| B | RNA-directed RNA polymerase catalytic subunit (EC 2.7.7.48) | protein | 752 | 46% helix, 16% strand | H6QM91 |
| C | Polymerase basic protein 2 | protein | 748 | 36% helix, 23% strand | H6QM90 |
| D | Polymerase acidic protein | protein | 708 | 44% helix, 18% strand | H6QM92 |
| E | RNA-directed RNA polymerase catalytic subunit (EC 2.7.7.48) | protein | 749 | 47% helix, 15% strand | H6QM91 |
| F | Polymerase basic protein 2 | protein | 746 | 36% helix, 23% strand | H6QM90 |
| N, M | RNA (5'-D(*(GDM))-R(P*AP*AP*U)-3') | rna | 3 | — | — |
| R, S | RNA (5'-R(*UP*AP*UP*AP*CP*CP*UP*CP*UP*GP*CP*UP*U)-3') | rna | 12 | — | — |
| U, V | RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*AP*GP*G)- 3') | rna | 15 | — | — |
Ligands and binding sites
- 8NK · 7-methylguanosine 5'-diphosphate · ligand · 2 copies · chains F, N, C, M
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 | 1192 | 0.89 | 0.91 | 136 | 8NK |
| 2 | 869 | 0.88 | 0.90 | 103 | empty |
| 3 | 1130 | 0.87 | 0.88 | 120 | empty |
| 4 | 850 | 0.85 | 0.87 | 84 | empty |
| 5 | 593 | 0.81 | 0.87 | 66 | empty |
Interfaces
22 interfaces between chains.
- A–B · 9174 Ų buried · 141 hydrogen bonds · protein-protein
- D–E · 9146 Ų buried · 136 hydrogen bonds · protein-protein
- E–F · 8179 Ų buried · 98 hydrogen bonds · protein-protein
- B–C · 8159 Ų buried · 95 hydrogen bonds · protein-protein
- D–F · 1629 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6EVJ · Crystal structure of bat influenza A/H17N10 polymerase with viral RNA promoter and capped… · 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 H6QM92
- Every structure of UniProt H6QM91
- Every structure of UniProt H6QM90
- Elsewhere: RCSB PDB 6EVJ · PDBe 6EVJ · UniProt H6QM92 · UniProt H6QM91 · UniProt H6QM90
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