MolNFT v1 · #136148 · protein
Cryoem structure of an influenza virus receptor-binding site antibody- antigen interface - class 1
5UJZ · Hemagglutinin HA1: “Cryoem structure of an influenza virus receptor-binding site antibody- antigen interface - class 1”. Electron microscopy, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.83). MolNFT v1 #136148 on GenesisL1…
- PDB
- 5UJZ
- 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 0.83
Structure
electron microscopy · 3 distinct chains · 16% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin HA1 | protein | 323 | 7% helix, 37% strand | A7UPX0 |
| B, D, F | Hemagglutinin HA2 | protein | 173 | 49% helix, 16% strand | A7UPX0 |
| G, H, I | Scfv | protein | 236 | 3% helix, 49% 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1022 | 0.83 | 0.84 | 120 | empty |
| 2 | 1004 | 0.83 | 0.84 | 117 | empty |
| 3 | 199 | 0.82 | 0.95 | 42 | empty |
| 4 | 121 | 0.76 | 0.95 | 16 | empty |
| 5 | 457 | 0.76 | 0.85 | 50 | empty |
Interfaces
18 interfaces between chains.
- A–B · 2825 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 2823 Ų buried · 45 hydrogen bonds · protein-protein
- E–F · 2769 Ų buried · 40 hydrogen bonds · protein-protein
- B–F · 1434 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 1359 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 glycan, 21 disulfide (N-glycosylation, disulfide).
Compared structures
- 5UJZ · CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface… · 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 A7UPX0
- Elsewhere: RCSB PDB 5UJZ · PDBe 5UJZ · UniProt A7UPX0
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