MolNFT v1 · #169891 · protein
Human antibody S8V2-47 in complex with the influenza hemagglutinin head domain of A/BEIJING/262/1995(H1N1)
6XQ4: “Human antibody S8V2-47 in complex with the influenza hemagglutinin head domain of A/BEIJING/262/1995(H1N1)”. X-ray diffraction, 2 ligands (NAG, BMA), 18 pockets (best druggability 0.61). MolNFT v1 #169891 on GenesisL1: 3D structure…
- PDB
- 6XQ4
- Type
- protein
- Length
- 1,303 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Antibody S8V2-47 light chain; Antibody S8V2-47 heavy chain
- UniProt
- B4UPF7
- Ligands
- NAG, BMA
- Pockets
- 18 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 209 | 11% helix, 38% strand | B4UPF7 |
| D | Hemagglutinin | protein | 212 | 12% helix, 35% strand | B4UPF7 |
| B, F | Antibody S8V2-47 light chain | protein | 218 | 5% helix, 48% strand | — |
| C, E | Antibody S8V2-47 heavy chain | protein | 223 | 7% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, D
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 554 | 0.61 | 0.74 | 55 | empty |
| 2 | 532 | 0.60 | 0.74 | 56 | empty |
| 3 | 126 | 0.50 | 0.80 | 19 | empty |
| 4 | 108 | 0.45 | 0.78 | 20 | empty |
| 5 | 125 | 0.42 | 0.76 | 28 | empty |
Interfaces
7 interfaces between chains.
- B–C · 2039 Ų buried · 10 hydrogen bonds · protein-protein
- F–E · 2024 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 477 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 441 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 435 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6XQ4 · Human antibody S8V2-47 in complex with the influenza hemagglutinin head domain of… · 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 B4UPF7
- Elsewhere: RCSB PDB 6XQ4 · PDBe 6XQ4 · UniProt B4UPF7
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