Research workbench
Crystal structure of broadly neutralizing antibody 3I14-D93N mutant bound to the influenza a H6 hemagglutinin
Analyse Crystal structure of broadly neutralizing antibody 3I14-D93N mutant bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WEX
- Type
- protein
- Length
- 933 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Hemagglutinin HA2 chain; Heavy chain; Light chain
- UniProt
- A0A0M3KL64, A0A0J9X245
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Hemagglutinin | protein | 325 | 8% helix, 37% strand | A0A0M3KL64 |
| F | Hemagglutinin HA2 chain | protein | 172 | 51% helix, 13% strand | A0A0J9X245 |
| H | Heavy chain | protein | 223 | 3% helix, 39% strand | — |
| L | Light chain | protein | 213 | 6% helix, 40% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 195 | 0.76 | 0.91 | 37 | empty |
| 2 | 67 | 0.71 | 0.96 | 22 | empty |
| 3 | 700 | 0.67 | 0.76 | 57 | empty |
| 4 | 496 | 0.64 | 0.77 | 57 | empty |
| 5 | 53 | 0.58 | 0.91 | 21 | empty |
Interfaces
5 interfaces between chains.
- E–F · 2749 Ų buried · 32 hydrogen bonds · protein-protein
- H–L · 2070 Ų buried · 10 hydrogen bonds · protein-protein
- F–H · 454 Ų buried · 2 hydrogen bonds · protein-protein
- F–L · 320 Ų buried · 3 hydrogen bonds · protein-protein
- E–H · 208 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 10 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6WEX · Crystal Structure of Broadly Neutralizing Antibody 3I14-D93N Mutant Bound to the… · the same entry in another collection · chain E against E, 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 A0A0M3KL64
- Every structure of UniProt A0A0J9X245
- Elsewhere: RCSB PDB 6WEX · PDBe 6WEX · UniProt A0A0M3KL64 · UniProt A0A0J9X245
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