MolNFT v1 · #136150 · protein
Cryoem structure of an influenza virus receptor-binding site antibody- antigen interface - class 3
5UK1 · Hemagglutinin HA1: “Cryoem structure of an influenza virus receptor-binding site antibody- antigen interface - class 3”. Electron microscopy, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.87). MolNFT v1 #136150 on GenesisL1…
- PDB
- 5UK1
- Type
- protein
- Length
- 2,196 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1; Hemagglutinin HA2; Scfv
- UniProt
- A7UPX0
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 16% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin HA1 | protein | 323 | 7% helix, 34% strand | A7UPX0 |
| B, D, F | Hemagglutinin HA2 | protein | 173 | 49% helix, 15% strand | A7UPX0 |
| G, H, I | Scfv | protein | 236 | 3% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 30 copies · chains A, C, E, B, D, F
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 450 | 0.87 | 0.94 | 58 | empty |
| 2 | 987 | 0.85 | 0.86 | 114 | empty |
| 3 | 563 | 0.78 | 0.85 | 59 | empty |
| 4 | 292 | 0.78 | 0.90 | 33 | empty |
| 5 | 506 | 0.78 | 0.85 | 58 | empty |
Interfaces
18 interfaces between chains.
- A–B · 2795 Ų buried · 45 hydrogen bonds · protein-protein
- E–F · 2776 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 2762 Ų buried · 40 hydrogen bonds · protein-protein
- B–F · 1250 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 1246 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 glycan, 21 disulfide (N-glycosylation, disulfide).
Compared structures
- 5UK1 · CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface… · the same entry in another collection · chain D against D, 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 A7UPX0
- Elsewhere: RCSB PDB 5UK1 · PDBe 5UK1 · UniProt A7UPX0
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