Research workbench
Cryo-EM structure of the ha trimer of A/BEIJING/262/1995(H1N1) in complex with neutralizing antibody 12H5
Analyse Cryo-EM structure of the ha trimer of A/BEIJING/262/1995(H1N1) 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
- 7YHK
- Type
- protein
- Length
- 604 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 12H5 light chain; 12H5 heavy chain; Hemagglutinin
- UniProt
- Q6WG01
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.61
Structure
electron microscopy · 3 distinct chains · 12% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | 12H5 light chain | protein | 116 | 3% helix, 49% strand | — |
| H | 12H5 heavy chain | protein | 111 | 3% helix, 50% strand | — |
| A | Hemagglutinin | protein | 377 | 18% helix, 31% strand | Q6WG01 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 406 | 0.61 | 0.76 | 41 | empty |
| 2 | 79 | 0.50 | 0.84 | 20 | empty |
| 3 | 193 | 0.48 | 0.76 | 45 | empty |
| 4 | 105 | 0.35 | 0.74 | 24 | empty |
| 5 | 68 | 0.35 | 0.77 | 16 | empty |
Interfaces
3 interfaces between chains.
- F–H · 809 Ų buried · 5 hydrogen bonds · protein-protein
- F–A · 432 Ų buried · 9 hydrogen bonds · protein-protein
- H–A · 403 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 7YHK · Cryo-EM structure of the HA trimer of A/Beijing/262/1995(H1N1) in complex with… · the same entry in another collection · chain F against F, 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 Q6WG01
- Elsewhere: RCSB PDB 7YHK · PDBe 7YHK · UniProt Q6WG01
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