MolNFT v1 · #180036 · protein
Localized reconstruction of the H1 A/MICHIGAN/45/2015 ectodomain displayed at the surface of I53_DN5 nanoparticle
7KNA · HEMAGGLUTININ,I53_DN5: “Localized reconstruction of the H1 A/MICHIGAN/45/2015 ectodomain displayed at the surface of I53_DN5…”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.80). MolNFT v1 #180036 on…
- PDB
- 7KNA
- Type
- protein
- Length
- 1,449 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HEMAGGLUTININ,I53_DN5
- UniProt
- A0A1J0CXU0
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 1 distinct chain · 23% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | HEMAGGLUTININ,I53_DN5 | protein | 483 | 23% helix, 30% strand | A0A1J0CXU0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 148 | 0.80 | 0.96 | 24 | empty |
| 2 | 195 | 0.79 | 0.93 | 26 | empty |
| 3 | 367 | 0.76 | 0.87 | 55 | empty |
| 4 | 265 | 0.73 | 0.87 | 38 | empty |
| 5 | 274 | 0.63 | 0.81 | 34 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2196 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 2194 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 2190 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 18 glycan (disulfide, N-glycosylation).
Compared structures
- 7KNA · Localized reconstruction of the H1 A/Michigan/45/2015 ectodomain displayed at the surface… · 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 A0A1J0CXU0
- Elsewhere: RCSB PDB 7KNA · PDBe 7KNA · UniProt A0A1J0CXU0
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