MolNFT v1 · #84214 · protein
R416A monomeric nucleoprotein of influenza a virus
3ZDP · Nucleocapsid protein: “R416A monomeric nucleoprotein of influenza a virus”. X-ray diffraction, 1 ligand (K), 20 pockets (best druggability 0.86). MolNFT v1 #84214 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3ZDP
- Type
- protein
- Length
- 1,391 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleocapsid protein
- UniProt
- Q1K9H2
- Ligands
- K
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleocapsid protein | protein | 462 | 45% helix, 10% strand | Q1K9H2 |
| B | Nucleocapsid protein | protein | 467 | 46% helix, 10% strand | Q1K9H2 |
| C | Nucleocapsid protein | protein | 462 | 47% helix, 11% strand | Q1K9H2 |
Ligands and binding sites
- K · Potassium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 478 | 0.86 | 0.93 | 106 | empty |
| 2 | 817 | 0.76 | 0.80 | 85 | empty |
| 3 | 295 | 0.72 | 0.85 | 47 | empty |
| 4 | 161 | 0.70 | 0.90 | 40 | empty |
| 5 | 787 | 0.70 | 0.76 | 81 | empty |
Interfaces
3 interfaces between chains.
- B–C · 908 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 881 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 875 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3ZDP · R416A Monomeric nucleoprotein of 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 Q1K9H2
- Elsewhere: RCSB PDB 3ZDP · PDBe 3ZDP · UniProt Q1K9H2
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