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Cryoem structure of influenza hemagglutinin A/VICTORIA/361/2011 in complex with cyno antibody 3B10
Analyse Cryoem structure of influenza hemagglutinin A/VICTORIA/361/2011 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WZT
- Type
- protein
- Length
- 2,799 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Cyno antibody heavy chain; Cyno antibody light chain
- UniProt
- A0A075EV12
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 3 distinct chains · 14% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Hemagglutinin | protein | 494 | 22% helix, 27% strand | A0A075EV12 |
| H, E, G | Cyno antibody heavy chain | protein | 225 | 4% helix, 44% strand | — |
| L, D, F | Cyno antibody light chain | protein | 214 | 7% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 39 copies · chains A, B, C
- BMA · beta-D-mannopyranose · sugar · 12 copies · chains B, C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 605 | 0.79 | 0.85 | 38 | empty |
| 2 | 1045 | 0.77 | 0.79 | 102 | empty |
| 3 | 727 | 0.76 | 0.81 | 70 | empty |
| 4 | 714 | 0.74 | 0.80 | 57 | empty |
| 5 | 399 | 0.72 | 0.83 | 41 | empty |
Interfaces
12 interfaces between chains.
- A–B · 2253 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 2243 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 2242 Ų buried · 17 hydrogen bonds · protein-protein
- H–L · 2121 Ų buried · 13 hydrogen bonds · protein-protein
- G–F · 2050 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 33 disulfide, 21 glycan (disulfide, N-glycosylation).
Compared structures
- 6WZT · CryoEM structure of influenza hemagglutinin A/Victoria/361/2011 in complex with cyno… · the same entry in another collection · chain G against G, 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 A0A075EV12
- Elsewhere: RCSB PDB 6WZT · PDBe 6WZT · UniProt A0A075EV12
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