MolNFT v1 · #91841 · protein
Crystal structure of broadly neutralizing antibody C05 bound to H3 influenza hemagglutinin, HA1 subunit
4FP8 · Hemagglutinin HA1 chain: “Crystal structure of broadly neutralizing antibody C05 bound to H3 influenza hemagglutinin, HA1 subunit”. X-ray diffraction, 2 ligands (NAG, ZN), 20 pockets (best druggability 0.75). MolNFT v1 #91841 on…
- 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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