Research workbench
Crystal structure of multidonor HV6-1-class broadly neutralizing influenza a antibody 56.A.09 in complex with hemagglutinin hong kong 1968.
Analyse Crystal structure of multidonor HV6-1-class broadly neutralizing influenza a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K9K
- Type
- protein
- Length
- 1,867 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 56.A.09 heavy chain; 56.A.09 light chain; Hemagglutinin
- UniProt
- Q91MA7
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.62
Structure
x-ray diffraction · 5 distinct chains · 18% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 56.A.09 heavy chain | protein | 226 | 5% helix, 57% strand | — |
| B, L | 56.A.09 light chain | protein | 215 | 7% helix, 53% strand | — |
| I | Hemagglutinin | protein | 490 | 26% helix, 31% strand | Q91MA7 |
| H | 56.A.09 heavy chain | protein | 224 | 5% helix, 56% strand | — |
| F | Hemagglutinin | protein | 497 | 26% helix, 27% strand | Q91MA7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, I, B, F, H, L
- MAN · alpha-D-mannopyranose · sugar · 15 copies · chains A, B, I, H, L
- BMA · beta-D-mannopyranose · sugar · 9 copies · chains I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 495 | 0.62 | 0.76 | 51 | empty |
| 2 | 373 | 0.61 | 0.78 | 42 | empty |
| 3 | 266 | 0.59 | 0.79 | 36 | empty |
| 4 | 342 | 0.59 | 0.77 | 43 | empty |
| 5 | 319 | 0.54 | 0.75 | 36 | empty |
Interfaces
9 interfaces between chains.
- H–L · 1835 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1830 Ų buried · 12 hydrogen bonds · protein-protein
- H–F · 613 Ų buried · 6 hydrogen bonds · protein-protein
- A–I · 600 Ų buried · 6 hydrogen bonds · protein-protein
- L–F · 427 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 disulfide, 13 glycan (disulfide, N-glycosylation).
Compared structures
- 5K9K · Crystal structure of multidonor HV6-1-class broadly neutralizing Influenza A antibody… · the same entry in another collection · chain B against B, 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 Q91MA7
- Elsewhere: RCSB PDB 5K9K · PDBe 5K9K · UniProt Q91MA7
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