MolNFT v1 · #152458 · protein
Crystal structure of H7 hemagglutinin from A/ANHUI/1/2013 in complex with a human neutralizing antibody L3A-44
6II9: “Crystal structure of H7 hemagglutinin from A/ANHUI/1/2013 in complex with a human neutralizing antibody L3A-44”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.86). MolNFT v1 #152458 on GenesisL1: 3D structure…
- PDB
- 6II9
- Type
- protein
- Length
- 2,740 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Heavy chain of L3A-44 Fab; Light chain of L3A-44 Fab
- UniProt
- A0A024CX39, A0A0K1LUI9
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 11% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 317 | 9% helix, 40% strand | A0A024CX39 |
| B, D, F | Hemagglutinin | protein | 170 | 50% helix, 12% strand | A0A0K1LUI9 |
| C, E | Hemagglutinin | protein | 316 | 7% helix, 40% strand | A0A024CX39 |
| H, P | Heavy chain of L3A-44 Fab | protein | 216 | 3% helix, 47% strand | — |
| L, N, Q | Light chain of L3A-44 Fab | protein | 212 | 6% helix, 45% strand | — |
| M | Heavy chain of L3A-44 Fab | protein | 213 | 4% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 908 | 0.86 | 0.88 | 98 | empty |
| 2 | 211 | 0.84 | 0.97 | 24 | empty |
| 3 | 159 | 0.80 | 0.96 | 27 | empty |
| 4 | 145 | 0.79 | 0.96 | 26 | empty |
| 5 | 141 | 0.78 | 0.96 | 26 | empty |
Interfaces
24 interfaces between chains.
- E–F · 3266 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 3212 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 3151 Ų buried · 46 hydrogen bonds · protein-protein
- H–L · 1634 Ų buried · 13 hydrogen bonds · protein-protein
- M–N · 1628 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6II9 · Crystal structure of H7 hemagglutinin from A/Anhui/1/2013 in complex with a human… · 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 A0A024CX39
- Every structure of UniProt A0A0K1LUI9
- Elsewhere: RCSB PDB 6II9 · PDBe 6II9 · UniProt A0A024CX39 · UniProt A0A0K1LUI9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.