Research workbench
Influenza strain PH1N1 2009 polymerase subunit pa endonuclease
Analyse Influenza strain PH1N1 2009 polymerase subunit pa endonuclease in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AVQ
- Type
- protein
- Length
- 771 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polymerase pa
- UniProt
- C3W5S0
- Ligands
- MN, MG
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase pa | protein | 196 | 49% helix, 16% strand | C3W5S0 |
| B | Polymerase pa | protein | 194 | 50% helix, 16% strand | C3W5S0 |
| C | Polymerase pa | protein | 191 | 50% helix, 16% strand | C3W5S0 |
| D | Polymerase pa | protein | 190 | 50% helix, 16% strand | C3W5S0 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 711 | 0.76 | 0.81 | 64 | empty |
| 2 | 522 | 0.74 | 0.82 | 48 | empty |
| 3 | 411 | 0.62 | 0.77 | 42 | MG |
| 4 | 427 | 0.62 | 0.76 | 42 | MG |
| 5 | 382 | 0.60 | 0.76 | 41 | MG |
Interfaces
4 interfaces between chains.
- B–C · 852 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 835 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 407 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 405 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4AVQ · Influenza strain pH1N1 2009 polymerase subunit PA endonuclease · 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 4AVQ · PDBe 4AVQ · UniProt C3W5S0
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