MolNFT v1 · #169885 · protein
Human antibody S1V2-58 in complex with the influenza hemagglutinin head domain of A/TEXAS/50/2012(H3N2)
6XPY: “Human antibody S1V2-58 in complex with the influenza hemagglutinin head domain of A/TEXAS/50/2012(H3N2)”. X-ray diffraction, 2 ligands (NAG, BMA), 6 pockets (best druggability 0.62). MolNFT v1 #169885 on GenesisL1: 3D structure…
- PDB
- 6XPY
- Type
- protein
- Length
- 711 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Fab light chain; Fab heavy chain
- UniProt
- R4L1D1
- Ligands
- NAG, BMA
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 271 | 11% helix, 36% strand | R4L1D1 |
| C | Fab light chain | protein | 212 | 4% helix, 50% strand | — |
| B | Fab heavy chain | protein | 228 | 5% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 598 | 0.62 | 0.74 | 56 | empty |
| 2 | 129 | 0.60 | 0.85 | 26 | empty |
| 3 | 283 | 0.59 | 0.78 | 44 | empty |
| 4 | 153 | 0.44 | 0.75 | 21 | empty |
| 5 | 108 | 0.36 | 0.74 | 23 | empty |
Interfaces
3 interfaces between chains.
- C–B · 2168 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 656 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 293 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6XPY · Human antibody S1V2-58 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 R4L1D1
- Elsewhere: RCSB PDB 6XPY · PDBe 6XPY · UniProt R4L1D1
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