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Structure of the midlink and cap-binding domains of influenza a polymerase PB2 subunit with a bound azaindole cap-binding inhibitor (vx-787)
Analyse Structure of the midlink and cap-binding domains of influenza a polymerase PB2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EUV
- Type
- protein
- Length
- 1,113 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polymerase basic protein 2
- UniProt
- P31345
- Ligands
- 21G, NI
- Pockets
- 14 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase basic protein 2 | protein | 277 | 30% helix, 30% strand | P31345 |
| C | Polymerase basic protein 2 | protein | 283 | 30% helix, 31% strand | P31345 |
| F | Polymerase basic protein 2 | protein | 275 | 31% helix, 31% strand | P31345 |
| I | Polymerase basic protein 2 | protein | 278 | 30% helix, 32% strand | P31345 |
Ligands and binding sites
- 21G · (2S,3S)-3-[[5-fluoranyl-2-(5-fluoranyl-1H-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-4-yl]amino]bicyclo[2.2.2]octane-2-carboxylic acid · ligand · 6 copies · chains A, I, C, F
- NI · Nickel (II) ion · metal · 4 copies · chains A, C, F, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1037 | 0.87 | 0.87 | 106 | 21G, NI |
| 2 | 551 | 0.82 | 0.88 | 60 | 21G, NI |
| 3 | 596 | 0.79 | 0.85 | 53 | 21G, NI |
| 4 | 354 | 0.71 | 0.84 | 51 | empty |
| 5 | 471 | 0.59 | 0.74 | 49 | empty |
Interfaces
6 interfaces between chains.
- C–F · 1049 Ų buried · 19 hydrogen bonds · protein-protein
- A–I · 1028 Ų buried · 16 hydrogen bonds · protein-protein
- F–I · 354 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 331 Ų buried · 6 hydrogen bonds · protein-protein
- C–I · 150 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6EUV · Structure of the midlink and cap-binding domains of influenza A polymerase PB2 subunit… · 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 P31345
- Elsewhere: RCSB PDB 6EUV · PDBe 6EUV · UniProt P31345
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