MolNFT v1 · #152457 · protein
Crystal structure of H7 hemagglutinin from A/ANHUI/1/2013 in complex with a human neutralizing antibody L4B-18
6II8: “Crystal structure of H7 hemagglutinin from A/ANHUI/1/2013 in complex with a human neutralizing antibody L4B-18”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.86). MolNFT v1 #152457 on GenesisL1: 3D structure…
- PDB
- 6II8
- Type
- protein
- Length
- 2,547 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Heavy chain of L4B-18 Fab; Light chain of L4B-18 Fab
- UniProt
- A0A024CX39, A0A0K1LUI9
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 8 distinct chains · 15% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin | protein | 316 | 8% helix, 41% strand | A0A024CX39 |
| B, D | Hemagglutinin | protein | 172 | 52% helix, 12% strand | A0A0K1LUI9 |
| F | Hemagglutinin | protein | 171 | 51% helix, 13% strand | A0A0K1LUI9 |
| J | Heavy chain of L4B-18 Fab | protein | 118 | 3% helix, 42% strand | — |
| K | Light chain of L4B-18 Fab | protein | 100 | 6% helix, 40% strand | — |
| G | Heavy chain of L4B-18 Fab | protein | 223 | 1% helix, 47% strand | — |
| H | Heavy chain of L4B-18 Fab | protein | 217 | 4% helix, 50% strand | — |
| I, L | Light chain of L4B-18 Fab | protein | 213 | 5% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B, C, D, 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 | 917 | 0.86 | 0.88 | 109 | empty |
| 2 | 222 | 0.84 | 0.96 | 23 | empty |
| 3 | 139 | 0.80 | 0.97 | 26 | empty |
| 4 | 984 | 0.79 | 0.81 | 102 | empty |
| 5 | 115 | 0.78 | 0.97 | 23 | empty |
Interfaces
24 interfaces between chains.
- E–F · 3225 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 3216 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 3185 Ų buried · 48 hydrogen bonds · protein-protein
- G–I · 1745 Ų buried · 17 hydrogen bonds · protein-protein
- H–L · 1737 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 6II8 · 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 6II8 · PDBe 6II8 · UniProt A0A024CX39 · UniProt A0A0K1LUI9
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