Research workbench
C-terminal domain of influenza polymerase pa subunit and optimized small peptide inhibitor
Analyse C-terminal domain of influenza polymerase pa subunit and optimized small… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SYI
- Type
- protein
- Length
- 432 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polymerase acidic protein; PB1-11
- EC
- 3.1.-.-
- UniProt
- D4HIS2
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase acidic protein (EC 3.1.-.-) | protein | 422 | 42% helix, 21% strand | D4HIS2 |
| B | PB1-11 | protein | 10 | 60% helix, 10% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 532 | 0.69 | 0.79 | 73 | PGE, EDO |
| 2 | 89 | 0.37 | 0.75 | 12 | empty |
| 3 | 60 | 0.34 | 0.77 | 15 | empty |
| 4 | 66 | 0.31 | 0.75 | 22 | EDO |
| 5 | 65 | 0.29 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1012 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6SYI · C-terminal domain of influenza polymerase pa subunit and optimized small peptide inhibitor · 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 D4HIS2
- Elsewhere: RCSB PDB 6SYI · PDBe 6SYI · UniProt D4HIS2
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