Research workbench
Crystal structure of polymerase acid protein (pa) from influenza a virus, wilson-SMITH/1933 (H1N1) bound to fragment hit ebsi-2643 5- [(4-CHLOROPHENYL)METHYL]-1,3,4-oxadiazol-2-amine
Analyse Crystal structure of polymerase acid protein (pa) from influenza a virus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IF8
- Type
- protein
- Length
- 402 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polymerase acidic protein
- UniProt
- P15659
- Ligands
- 6AX, CL
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase acidic protein | protein | 402 | 45% helix, 19% strand | P15659 |
Ligands and binding sites
- 6AX · 5-[(4-chlorophenyl)methyl]-1,3,4-oxadiazol-2-amine · ligand · chains A
- CL · Chloride ion · ion · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
- EDO · 1,2-ethanediol · additive · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 221 | 0.65 | 0.83 | 31 | DMS |
| 2 | 117 | 0.38 | 0.74 | 24 | GOL |
| 3 | 127 | 0.38 | 0.73 | 17 | empty |
| 4 | 104 | 0.35 | 0.74 | 23 | empty |
| 5 | 57 | 0.32 | 0.76 | 16 | empty |
Compared structures
- 5IF8 · Crystal structure of polymerase acid protein (PA) from Influenza A virus… · 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 P15659
- Elsewhere: RCSB PDB 5IF8 · PDBe 5IF8 · UniProt P15659
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