MolNFT v1 · #169887 · protein
Human antibody S8V2-18 in complex with the influenza hemagglutinin head domain of A/CALIFORNIA/7/2009(NYMC-X181)(H1N1)
6XQ0: “Human antibody S8V2-18 in complex with the influenza hemagglutinin head domain of…”. X-ray diffraction, 3 ligands (NAG, FUC, BMA), 15 pockets (best druggability 0.74). MolNFT v1 #169887 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6XQ0
- Type
- protein
- Length
- 1,321 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Antibody S8V2-18 light chain; Antibody S8V2-18 heavy chain
- UniProt
- I6T519
- Ligands
- NAG, FUC, BMA
- Pockets
- 15 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Hemagglutinin | protein | 216 | 10% helix, 37% strand | I6T519 |
| A | Hemagglutinin | protein | 219 | 11% helix, 37% strand | I6T519 |
| C, F | Antibody S8V2-18 light chain | protein | 213 | 8% helix, 52% strand | — |
| B, E | Antibody S8V2-18 heavy chain | protein | 230 | 8% helix, 55% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains D, A, F
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains D, A, F
- BMA · beta-D-mannopyranose · sugar · 2 copies
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 932 | 0.74 | 0.78 | 97 | empty |
| 2 | 768 | 0.67 | 0.75 | 64 | empty |
| 3 | 245 | 0.59 | 0.79 | 36 | empty |
| 4 | 53 | 0.56 | 0.90 | 20 | empty |
| 5 | 242 | 0.55 | 0.77 | 36 | empty |
Interfaces
9 interfaces between chains.
- E–F · 1932 Ų buried · 13 hydrogen bonds · protein-protein
- C–B · 1845 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 828 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 814 Ų buried · 15 hydrogen bonds · protein-protein
- C–F · 340 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6XQ0 · Human antibody S8V2-18 in complex with the influenza hemagglutinin head domain of… · the same entry in another collection · chain D against D, 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 I6T519
- Elsewhere: RCSB PDB 6XQ0 · PDBe 6XQ0 · UniProt I6T519
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