Research workbench
Crystal structure of Fab 39.29 in complex with influenza hemagglutinin A/PERTH/16/2009 (H3N2)
Analyse Crystal structure of Fab 39.29 in complex with influenza hemagglutinin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KVN
- Type
- protein
- Length
- 899 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Human IgG heavy chain; Human IgG light chain
- UniProt
- C6KNH7
- Ligands
- NAG, BMA, PO4
- Pockets
- 8 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 470 | 24% helix, 31% strand | C6KNH7 |
| H | Human IgG heavy chain | protein | 216 | 1% helix, 45% strand | — |
| L | Human IgG light chain | protein | 213 | 6% helix, 53% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, H, L
- BMA · beta-D-mannopyranose · sugar · 2 copies
- PO4 · Phosphate ion · ion · chains L
- PGE · Triethylene glycol · additive · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 477 | 0.64 | 0.77 | 59 | empty |
| 2 | 244 | 0.61 | 0.80 | 35 | empty |
| 3 | 63 | 0.57 | 0.89 | 18 | empty |
| 4 | 306 | 0.52 | 0.74 | 41 | PGE |
| 5 | 75 | 0.32 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1701 Ų buried · 12 hydrogen bonds · protein-protein
- A–L · 748 Ų buried · 15 hydrogen bonds · protein-protein
- A–H · 529 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 4KVN · Crystal structure of Fab 39.29 in complex with Influenza Hemagglutinin A/Perth/16/2009… · 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 C6KNH7
- Elsewhere: RCSB PDB 4KVN · PDBe 4KVN · UniProt C6KNH7
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