MolNFT v2 · #216898 · protein + RNA
Influenza A/H7N9 polymerase in elongation state with continuous Pol II pS5 CTD peptide mimic bound in site 1A/2A
8PNQ · Polymerase acidic protein: “Influenza A/H7N9 polymerase in elongation state with continuous Pol II pS5 CTD peptide mimic bound in site…”. Electron microscopy at 2.88, 2 ligands (2KH, MG), 20 pockets (best druggability 0.89). MolNFT…
- PDB
- 8PNQ
- Type
- protein + RNA
- Length
- 1,771 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.88
- Source
- Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)); SYNTHETIC CONSTRUCT
- Molecule
- Polymerase acidic protein; RNA-directed RNA polymerase catalytic subunit; Polymerase…
- UniProt
- M9TI86, S5ME50, X5F427
- Ligands
- 2KH, MG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · resolution 2.88 · 6 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase acidic protein | protein | 708 | 44% helix, 18% strand | M9TI86 |
| B | RNA-directed RNA polymerase catalytic subunit | protein | 744 | 46% helix, 16% strand | S5ME50 |
| C | Polymerase basic protein 2 | protein | 249 | 45% helix, 17% strand | X5F427 |
| V | 51-mer vRNA loop (v51_mut_S) | rna | 36 | — | — |
| M | Replication product | rna | 9 | — | — |
| G | RNA Pol II CTD 6 repeats (site 1A/2A) | protein | 25 | 0% helix, 0% strand | — |
Ligands and binding sites
- 2KH · 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine · ligand · chains B, V, M
- MG · Magnesium ion · metal · 2 copies · chains B, 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 | 801 | 0.89 | 0.93 | 114 | 2KH |
| 2 | 175 | 0.76 | 0.93 | 34 | empty |
| 3 | 222 | 0.76 | 0.91 | 43 | empty |
| 4 | 72 | 0.75 | 0.99 | 21 | empty |
| 5 | 1092 | 0.75 | 0.78 | 96 | empty |
Interfaces
12 interfaces between chains.
- A–B · 9021 Ų buried · 134 hydrogen bonds · protein-protein
- B–C · 6151 Ų buried · 57 hydrogen bonds · protein-protein
- B–V · 2832 Ų buried · 45 hydrogen bonds · protein-nucleic
- A–V · 2342 Ų buried · 43 hydrogen bonds · protein-nucleic
- A–C · 1175 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
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 M9TI86
- Every structure of UniProt S5ME50
- Every structure of UniProt X5F427
- Elsewhere: RCSB PDB 8PNQ · PDBe 8PNQ · UniProt M9TI86 · UniProt S5ME50 · UniProt X5F427
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