Research workbench
Influenza H5N1 nucleoprotein in complex with nucleotides
Analyse Influenza H5N1 nucleoprotein in complex with nucleotides in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DXP
- Type
- protein + RNA
- Length
- 820 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoprotein; RNA (5'-R(P*(OMU)P*(OMU)P*(OMU)P*(OMU))-3')
- Ligands
- OMU
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoprotein | protein | 399 | 51% helix, 9% strand | — |
| B | Nucleoprotein | protein | 418 | 51% helix, 9% strand | — |
| C | RNA (5'-R(P*(OMU)P*(OMU)P*(OMU)P*(OMU))-3') | rna | 3 | — | — |
Ligands and binding sites
- OMU · O2'-methyluridine 5'-monophosphate · ligand · chains B, C
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1114 | 0.80 | 0.81 | 107 | empty |
| 2 | 323 | 0.62 | 0.79 | 41 | EDO |
| 3 | 155 | 0.54 | 0.80 | 19 | empty |
| 4 | 299 | 0.54 | 0.75 | 30 | empty |
| 5 | 114 | 0.51 | 0.81 | 24 | empty |
Interfaces
2 interfaces between chains.
- A–B · 552 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 550 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 3 modified, 1 covalent (nucleotide modification, covalent ligand).
Compared structures
- 7DXP · Influenza H5N1 nucleoprotein in complex with nucleotides · 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
- Elsewhere: RCSB PDB 7DXP · PDBe 7DXP
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