MolNFT v1 · #78604 · protein
Crystal structure of broadly neutralizing antibody CR8020 bound to the influenza a H3 hemagglutinin
3SDY · Hemagglutinin HA1 chain: “Crystal structure of broadly neutralizing antibody CR8020 bound to the influenza a H3 hemagglutinin”. X-ray diffraction, 5 ligands (NAG, BMA, MAN), 7 pockets (best druggability 0.58). MolNFT v1 #78604 on…
- PDB
- 3SDY
- Type
- protein
- Length
- 927 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain; Antibody CR8020, heavy chain; Antibody…
- UniProt
- Q91MA7
- Ligands
- NAG, BMA, MAN, FUC, SO4
- Pockets
- 7 · best druggability 0.58
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin HA1 chain | protein | 319 | 10% helix, 41% strand | Q91MA7 |
| B | Hemagglutinin HA2 chain | protein | 172 | 55% helix, 14% strand | Q91MA7 |
| H | Antibody CR8020, heavy chain | protein | 221 | 7% helix, 49% strand | — |
| L | Antibody CR8020, light chain | protein | 215 | 8% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 4 copies
- MAN · alpha-D-mannopyranose · sugar · 4 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B, L
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 218 | 0.58 | 0.80 | 38 | empty |
| 2 | 360 | 0.58 | 0.76 | 36 | empty |
| 3 | 309 | 0.55 | 0.75 | 39 | empty |
| 4 | 301 | 0.52 | 0.74 | 51 | empty |
| 5 | 141 | 0.48 | 0.78 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2829 Ų buried · 33 hydrogen bonds · protein-protein
- H–L · 1827 Ų buried · 15 hydrogen bonds · protein-protein
- B–H · 603 Ų buried · 11 hydrogen bonds · protein-protein
- B–L · 202 Ų buried · 1 hydrogen bond · protein-protein
- A–H · 142 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 10 disulfide, 5 glycan, 1 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 3SDY · Crystal Structure of Broadly Neutralizing Antibody CR8020 Bound to the Influenza A H3… · 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 Q91MA7
- Elsewhere: RCSB PDB 3SDY · PDBe 3SDY · UniProt Q91MA7
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