Research workbench
Human antibody S1V2-83 in complex with the influenza hemagglutinin head domain of A/MOSCOW/10/1999(H3N2)
Analyse Human antibody S1V2-83 in complex with the influenza hemagglutinin head domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XPZ
- Type
- protein
- Length
- 1,425 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Antibody S1V2-83 heavy chain; Antibody S1V2-83 light chain
- UniProt
- Q1NZ37
- Ligands
- NAG, BMA
- Pockets
- 12 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 268 | 12% helix, 36% strand | Q1NZ37 |
| D | Hemagglutinin | protein | 269 | 12% helix, 34% strand | Q1NZ37 |
| B, E | Antibody S1V2-83 heavy chain | protein | 233 | 6% helix, 48% strand | — |
| C, F | Antibody S1V2-83 light chain | protein | 211 | 6% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, D, B
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 867 | 0.69 | 0.75 | 73 | empty |
| 2 | 404 | 0.57 | 0.75 | 46 | empty |
| 3 | 336 | 0.56 | 0.75 | 51 | empty |
| 4 | 109 | 0.49 | 0.80 | 26 | empty |
| 5 | 77 | 0.39 | 0.77 | 17 | empty |
Interfaces
8 interfaces between chains.
- B–C · 2061 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 2022 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 677 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 654 Ų buried · 9 hydrogen bonds · protein-protein
- D–B · 288 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 6XPZ · Human antibody S1V2-83 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 Q1NZ37
- Elsewhere: RCSB PDB 6XPZ · PDBe 6XPZ · UniProt Q1NZ37
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