MolNFT v1 · #149164 · protein
Influenza A/CALIFORNIA/04/2009 (PH1N1) endonuclease with bound inhibitor, baloxavir acid (bxa)
6FS6 · Polymerase acidic PROTEIN,POLYMERASE acidic protein: “Influenza A/CALIFORNIA/04/2009 (PH1N1) endonuclease with bound inhibitor, baloxavir acid (bxa)”. X-ray diffraction, 2 ligands (E4Z, MN), 15 pockets (best druggability 0.84).…
- PDB
- 6FS6
- Type
- protein
- Length
- 1,056 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polymerase acidic PROTEIN,POLYMERASE acidic protein
- EC
- 3.1.-.-
- UniProt
- C3W5S0
- Ligands
- E4Z, MN
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase acidic PROTEIN,POLYMERASE acidic protein (EC 3.1.-.-) | protein | 177 | 53% helix, 13% strand | C3W5S0 |
| B | Polymerase acidic PROTEIN,POLYMERASE acidic protein (EC 3.1.-.-) | protein | 176 | 54% helix, 13% strand | C3W5S0 |
| C | Polymerase acidic PROTEIN,POLYMERASE acidic protein (EC 3.1.-.-) | protein | 176 | 54% helix, 13% strand | C3W5S0 |
| D | Polymerase acidic PROTEIN,POLYMERASE acidic protein (EC 3.1.-.-) | protein | 176 | 55% helix, 13% strand | C3W5S0 |
| E | Polymerase acidic PROTEIN,POLYMERASE acidic protein (EC 3.1.-.-) | protein | 177 | 53% helix, 13% strand | C3W5S0 |
| F | Polymerase acidic PROTEIN,POLYMERASE acidic protein (EC 3.1.-.-) | protein | 174 | 53% helix, 13% strand | C3W5S0 |
Ligands and binding sites
- E4Z · Baloxavir acid · ligand · 6 copies · chains A, B, E, C, D, F
- MN · Manganese (II) ion · metal · 12 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.84 | 0.85 | 95 | MN, E4Z |
| 2 | 479 | 0.77 | 0.85 | 55 | MN, E4Z |
| 3 | 491 | 0.76 | 0.84 | 66 | MN, E4Z |
| 4 | 560 | 0.72 | 0.80 | 52 | MN, E4Z |
| 5 | 561 | 0.71 | 0.80 | 56 | MN, E4Z |
Interfaces
8 interfaces between chains.
- D–F · 775 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 766 Ų buried · 18 hydrogen bonds · protein-protein
- C–E · 764 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 616 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 616 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6FS6 · Influenza A/California/04/2009 (pH1N1) endonuclease with bound inhibitor, baloxavir acid… · 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 C3W5S0
- Elsewhere: RCSB PDB 6FS6 · PDBe 6FS6 · UniProt C3W5S0
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