MolNFT v1 · #140186 · protein
Crystal structure of a group 2 ha binding antibody AF4H1K1 Fab in complex with the H4N6 duck isolate (H4-CZ/56) hemagglutinin
5Y2M: “Crystal structure of a group 2 ha binding antibody AF4H1K1 Fab in complex with the H4N6 duck isolate…”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.87). MolNFT v1 #140186 on GenesisL1: 3D structure, binding…
- PDB
- 5Y2M
- Type
- protein
- Length
- 2,345 residues
- Chains
- 10
- 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
- A3KF09
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Hemagglutinin | protein | 319 | 9% helix, 39% strand | A3KF09 |
| D, E, F | Hemagglutinin | protein | 172 | 54% helix, 13% strand | A3KF09 |
| I, K | A group 2 ha binding antibody AF4H1K1 Fab heavy chain | protein | 224 | 7% helix, 48% strand | — |
| J, L | 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, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1029 | 0.87 | 0.88 | 111 | empty |
| 2 | 180 | 0.81 | 0.96 | 20 | empty |
| 3 | 440 | 0.80 | 0.88 | 52 | empty |
| 4 | 458 | 0.79 | 0.87 | 52 | empty |
| 5 | 636 | 0.75 | 0.82 | 76 | empty |
Interfaces
25 interfaces between chains.
- B–E · 2965 Ų buried · 46 hydrogen bonds · protein-protein
- C–F · 2964 Ų buried · 46 hydrogen bonds · protein-protein
- A–D · 2962 Ų buried · 46 hydrogen bonds · protein-protein
- K–L · 1906 Ų buried · 14 hydrogen bonds · protein-protein
- I–J · 1861 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 5Y2M · Crystal structure of a group 2 HA binding antibody AF4H1K1 Fab in complex with the H4N6… · 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 A3KF09
- Elsewhere: RCSB PDB 5Y2M · PDBe 5Y2M · UniProt A3KF09
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.