Research workbench
Human antibody S5V2-29 in complex with influenza hemagglutinin A/TEXAS/50/2012 (H3N2)
Analyse Human antibody S5V2-29 in complex with influenza hemagglutinin A/TEXAS/50/2012… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E4X
- Type
- protein
- Length
- 714 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; S5V2-29 light chain; S5V2-29 heavy chain
- UniProt
- R4L1D1, Q8TCD0
- Ligands
- NAG, BMA, FUC, MAN
- Pockets
- 6 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Hemagglutinin | protein | 275 | 11% helix, 38% strand | R4L1D1 |
| Y | S5V2-29 light chain | protein | 208 | 6% helix, 51% strand | Q8TCD0 |
| Z | S5V2-29 heavy chain | protein | 231 | 7% helix, 55% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains B
- BMA · beta-D-mannopyranose · sugar · 3 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains B
- MAN · alpha-D-mannopyranose · sugar
- GOL · Glycerol · additive · 4 copies · chains B, Y, Z
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.55 | 0.83 | 29 | empty |
| 2 | 203 | 0.52 | 0.77 | 27 | empty |
| 3 | 275 | 0.50 | 0.74 | 35 | empty |
| 4 | 129 | 0.44 | 0.77 | 23 | empty |
| 5 | 56 | 0.27 | 0.74 | 15 | empty |
Interfaces
3 interfaces between chains.
- Y–Z · 2003 Ų buried · 19 hydrogen bonds · protein-protein
- B–Z · 660 Ų buried · 4 hydrogen bonds · protein-protein
- B–Y · 255 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6E4X · Human antibody S5V2-29 in complex with influenza hemagglutinin A/Texas/50/2012 (H3N2) · the same entry in another collection · chain B against B, 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
- Every structure of UniProt Q8TCD0
- Elsewhere: RCSB PDB 6E4X · PDBe 6E4X · UniProt R4L1D1 · UniProt Q8TCD0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.