Research workbench
Crystal structure of broadly neutralizing antibody C05 bound to H3 influenza hemagglutinin, HA1 subunit
Analyse Crystal structure of broadly neutralizing antibody C05 bound to H3 influenza… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FP8
- Type
- protein
- Length
- 2,873 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Antibody C05, heavy chain; Antibody C05, light chain
- UniProt
- Q91MA7
- Ligands
- NAG, ZN
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hemagglutinin HA1 chain | protein | 267 | 12% helix, 42% strand | Q91MA7 |
| C | Hemagglutinin HA1 chain | protein | 265 | 12% helix, 40% strand | Q91MA7 |
| D | Hemagglutinin HA1 chain | protein | 266 | 12% helix, 42% strand | Q91MA7 |
| H, I, J, K | Antibody C05, heavy chain | protein | 239 | 10% helix, 49% strand | — |
| L, M, N, O | Antibody C05, light chain | protein | 213 | 6% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains C, A, D
- ZN · Zinc ion · metal · 8 copies · chains H, L, B, I, M, J, N, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 604 | 0.75 | 0.81 | 74 | empty |
| 2 | 445 | 0.69 | 0.80 | 30 | empty |
| 3 | 747 | 0.66 | 0.74 | 79 | empty |
| 4 | 611 | 0.64 | 0.75 | 67 | empty |
| 5 | 486 | 0.60 | 0.74 | 63 | empty |
Interfaces
17 interfaces between chains.
- J–N · 1924 Ų buried · 12 hydrogen bonds · protein-protein
- K–O · 1912 Ų buried · 10 hydrogen bonds · protein-protein
- I–M · 1880 Ų buried · 10 hydrogen bonds · protein-protein
- H–L · 1874 Ų buried · 10 hydrogen bonds · protein-protein
- C–J · 717 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide, 4 modified, 3 glycan (disulfide, cyclization, N-glycosylation).
Compared structures
- 4FP8 · Crystal structure of broadly neutralizing antibody C05 bound to H3 influenza… · 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 4FP8 · PDBe 4FP8 · UniProt Q91MA7
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