Research workbench
Crystal structure of avian influenza virus PA_N in complex with AMP
Analyse Crystal structure of avian influenza virus PA_N in complex with AMP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HW5
- Type
- protein
- Length
- 709 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polymerase acidic protein
- UniProt
- Q9Q0U9
- Ligands
- AMP, MG
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase acidic protein | protein | 177 | 53% helix, 13% strand | Q9Q0U9 |
| B | Polymerase acidic protein | protein | 180 | 52% helix, 13% strand | Q9Q0U9 |
| C, D | Polymerase acidic protein | protein | 176 | 52% helix, 13% strand | Q9Q0U9 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A
- 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
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 619 | 0.71 | 0.79 | 48 | MG, AMP |
| 2 | 520 | 0.70 | 0.79 | 46 | empty |
| 3 | 523 | 0.69 | 0.79 | 48 | MG |
| 4 | 487 | 0.65 | 0.77 | 44 | MG |
| 5 | 531 | 0.62 | 0.75 | 45 | empty |
Interfaces
4 interfaces between chains.
- A–B · 606 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 259 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 18 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 18 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3HW5 · crystal structure of avian influenza virus PA_N in complex with AMP · 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 Q9Q0U9
- Elsewhere: RCSB PDB 3HW5 · PDBe 3HW5 · UniProt Q9Q0U9
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