Research workbench
Crystal structure of WSN/A influenza nucleoprotein with bms-883559 ligand bound
Analyse Crystal structure of WSN/A influenza nucleoprotein with bms-883559 ligand bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DYB
- Type
- protein
- Length
- 852 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleocapsid protein
- UniProt
- B4URF1
- Ligands
- 0MH
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleocapsid protein | protein | 430 | 46% helix, 9% strand | B4URF1 |
| B | Nucleocapsid protein | protein | 422 | 49% helix, 9% strand | B4URF1 |
Ligands and binding sites
- 0MH · N-[4-chloranyl-5-[4-[[3-(2-methoxyphenyl)-5-methyl-1,2-oxazol-4-yl]carbonyl]piperazin-1-yl]-2-nitro-phenyl]thiophene-2-carboxamide · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 991 | 0.78 | 0.80 | 93 | 0MH |
| 2 | 1071 | 0.78 | 0.80 | 83 | empty |
| 3 | 743 | 0.74 | 0.79 | 64 | empty |
| 4 | 246 | 0.63 | 0.82 | 40 | empty |
| 5 | 100 | 0.37 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 586 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4DYB · Crystal Structure of WSN/A Influenza Nucleoprotein with BMS-883559 Ligand Bound · 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 B4URF1
- Elsewhere: RCSB PDB 4DYB · PDBe 4DYB · UniProt B4URF1
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