MolNFT v1 · #148804 · protein + RNA
Crystal structure of bat influenza A/H17N10 polymerase with viral RNA promoter bound to a 22-mer modified pol II ctd peptide with serine 5 thiophosphorylated.
6FHH · Polymerase acidic protein: “Crystal structure of bat influenza A/H17N10 polymerase with viral RNA promoter bound to a 22-mer modified pol…”. X-ray diffraction, 2 ligands (ZN, PO4), 20 pockets (best druggability 0.88). MolNFT v1…
- PDB
- 6FHH
- Type
- protein + RNA
- Length
- 2,229 residues
- Chains
- 7
- 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
- ZN, PO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 7 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase acidic protein | protein | 709 | 41% helix, 16% strand | H6QM92 |
| B | RNA-directed RNA polymerase catalytic subunit (EC 2.7.7.48) | protein | 750 | 46% helix, 17% strand | H6QM91 |
| C | Polymerase basic protein 2 | protein | 725 | 38% helix, 23% strand | H6QM90 |
| R | RNA (5'-R(*UP*AP*UP*AP*CP*CP*UP*CP*UP*GP*CP*UP*U)-3') | rna | 12 | — | — |
| V | RNA (5'- R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*AP*GP*GP*G)-3') | rna | 16 | — | — |
| X | Tyr-ser-pro-thr-tps-pro-ser | protein | 7 | 0% helix, 0% strand | — |
| Y | Tyr-ser-pro-thr-tps-pro-ser | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1013 | 0.88 | 0.89 | 99 | PO4 |
| 2 | 611 | 0.82 | 0.87 | 70 | empty |
| 3 | 621 | 0.81 | 0.86 | 71 | empty |
| 4 | 474 | 0.80 | 0.87 | 83 | empty |
| 5 | 767 | 0.79 | 0.83 | 53 | PO4 |
Interfaces
12 interfaces between chains.
- A–B · 9111 Ų buried · 155 hydrogen bonds · protein-protein
- B–C · 7490 Ų buried · 90 hydrogen bonds · protein-protein
- A–C · 1839 Ų buried · 14 hydrogen bonds · protein-protein
- A–V · 1341 Ų buried · 29 hydrogen bonds · protein-nucleic
- B–V · 842 Ų buried · 19 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 6FHH · Crystal structure of bat influenza A/H17N10 polymerase with viral RNA promoter bound to a… · the same entry in another collection · chain B against B, 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 6FHH · PDBe 6FHH · UniProt H6QM92 · UniProt H6QM91 · UniProt H6QM90
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