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In-situ structure of the trimeric hef from influenza C by flexible fitting into a cryo-et MAP.
Analyse In-situ structure of the trimeric hef from influenza C by flexible fitting into… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YI5
- Type
- protein
- Length
- 1,767 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin-esterase-fusion glycoprotein
- EC
- 3.1.1.53
- UniProt
- P07975
- Ligands
- NAG, BMA, NDG
- Pockets
- 13 · best druggability 0.86
Structure
electron microscopy · 2 distinct chains · 24% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, C | Hemagglutinin-esterase-fusion glycoprotein (EC 3.1.1.53) | protein | 427 | 15% helix, 36% strand | P07975 |
| B, F, D | Hemagglutinin-esterase-fusion glycoprotein (EC 3.1.1.53) | protein | 162 | 49% helix, 15% strand | P07975 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, B, C, E, F, D
- BMA · beta-D-mannopyranose · sugar · 9 copies · chains B, C, F, D
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 3 copies · chains B, C, A, F, E, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1012 | 0.86 | 0.87 | 112 | empty |
| 2 | 699 | 0.80 | 0.84 | 79 | NAG |
| 3 | 620 | 0.75 | 0.81 | 73 | empty |
| 4 | 121 | 0.62 | 0.86 | 24 | empty |
| 5 | 177 | 0.60 | 0.82 | 26 | empty |
Interfaces
9 interfaces between chains.
- C–D · 3460 Ų buried · 75 hydrogen bonds · protein-protein
- A–B · 3431 Ų buried · 73 hydrogen bonds · protein-protein
- E–F · 3400 Ų buried · 70 hydrogen bonds · protein-protein
- B–D · 514 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 435 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 6YI5 · In-situ structure of the trimeric HEF from influenza C by flexible fitting into a cryo-ET… · 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 P07975
- Elsewhere: RCSB PDB 6YI5 · PDBe 6YI5 · UniProt P07975
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