Research workbench
Crystal structure of a group 2 ha binding antibody AF4H1K1 Fab in complex with the 1968 H3N2 pandemic (H3-AC/68) hemagglutinin
Analyse Crystal structure of a group 2 ha binding antibody AF4H1K1 Fab in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y2L
- Type
- protein
- Length
- 916 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; A group 2 ha binding antibody AF4H1K1 Fab heavy chain; A group 2 ha…
- UniProt
- P03437
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.58
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 317 | 9% helix, 41% strand | P03437 |
| B | Hemagglutinin | protein | 163 | 54% helix, 13% strand | P03437 |
| I | A group 2 ha binding antibody AF4H1K1 Fab heavy chain | protein | 224 | 7% helix, 48% strand | — |
| J | A group 2 ha binding antibody AF4H1K1 Fab light chain | protein | 212 | 4% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 189 | 0.58 | 0.81 | 29 | empty |
| 2 | 128 | 0.50 | 0.80 | 28 | empty |
| 3 | 228 | 0.49 | 0.75 | 34 | empty |
| 4 | 139 | 0.45 | 0.77 | 26 | empty |
| 5 | 101 | 0.45 | 0.79 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2830 Ų buried · 36 hydrogen bonds · protein-protein
- I–J · 1831 Ų buried · 11 hydrogen bonds · protein-protein
- B–I · 579 Ų buried · 9 hydrogen bonds · protein-protein
- A–I · 479 Ų buried · 1 hydrogen bond · protein-protein
- B–J · 95 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5Y2L · Crystal structure of a group 2 HA binding antibody AF4H1K1 Fab in complex with the 1968… · 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 P03437
- Elsewhere: RCSB PDB 5Y2L · PDBe 5Y2L · UniProt P03437
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.