Research workbench
Crystal structure of avian influenza virus pan bound to compound 5
Analyse Crystal structure of avian influenza virus pan bound to compound 5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4E5J
- Type
- protein
- Length
- 722 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polymerase protein pa
- UniProt
- Q5EP34
- Ligands
- 581, MN, SO4
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Polymerase protein pa | protein | 181 | 55% helix, 13% strand | Q5EP34 |
| D | Polymerase protein pa | protein | 179 | 55% helix, 13% strand | Q5EP34 |
Ligands and binding sites
- 581 · 2-[3-(acetylamino)phenyl]-5-hydroxy-6-oxo-1,6-dihydropyrimidine-4-carboxylic acid · ligand · 8 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 577 | 0.69 | 0.78 | 56 | 581, MN |
| 2 | 644 | 0.68 | 0.77 | 46 | 581, MN |
| 3 | 583 | 0.68 | 0.77 | 49 | 581, MN |
| 4 | 543 | 0.67 | 0.78 | 49 | 581, MN |
| 5 | 91 | 0.38 | 0.76 | 15 | empty |
Interfaces
4 interfaces between chains.
- B–D · 621 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 611 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 603 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 588 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4E5J · Crystal structure of avian influenza virus PAn bound to compound 5 · 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 Q5EP34
- Elsewhere: RCSB PDB 4E5J · PDBe 4E5J · UniProt Q5EP34
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