Research workbench
Crystal structure of influenza a virus nucleoprotein with ligand
Analyse Crystal structure of influenza a virus nucleoprotein with ligand in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RO5
- Type
- protein
- Length
- 853 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleocapsid protein
- UniProt
- Q1K9H2
- Ligands
- LGH
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleocapsid protein | protein | 430 | 46% helix, 9% strand | Q1K9H2 |
| B | Nucleocapsid protein | protein | 423 | 49% helix, 9% strand | Q1K9H2 |
Ligands and binding sites
- LGH · [4-(2-chloro-4-nitrophenyl)piperazin-1-yl][3-(2-methoxyphenyl)-5-methyl-1,2-oxazol-4-yl]methanone · ligand · 2 copies · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1000 | 0.80 | 0.81 | 98 | LGH |
| 2 | 1039 | 0.78 | 0.80 | 85 | empty |
| 3 | 819 | 0.74 | 0.79 | 64 | empty |
| 4 | 61 | 0.41 | 0.81 | 13 | empty |
| 5 | 110 | 0.38 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 598 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3RO5 · Crystal structure of influenza A virus nucleoprotein with ligand · 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 Q1K9H2
- Elsewhere: RCSB PDB 3RO5 · PDBe 3RO5 · UniProt Q1K9H2
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