MolNFT v1 · #124286 · protein
Crystal structure of multidonor HV1-18-class broadly neutralizing influenza a antibody 16.G.07 in complex with A/HONG KONG/1-4-MA21- 1/1968 (H3N2) hemagglutinin
5KAN · Hemagglutinin HA1: “Crystal structure of multidonor HV1-18-class broadly neutralizing influenza a antibody 16.G.07 in complex…”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.84). MolNFT v1 #124286 on GenesisL1…
- PDB
- 5KAN
- Type
- protein
- Length
- 2,806 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1; Hemagglutinin HA2; 16.G.07 heavy chain; 16.G.07 light chain
- UniProt
- Q91MA7
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 25% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin HA1 | protein | 319 | 10% helix, 41% strand | Q91MA7 |
| B | Hemagglutinin HA2 | protein | 173 | 51% helix, 14% strand | Q91MA7 |
| D | Hemagglutinin HA2 | protein | 171 | 53% helix, 14% strand | Q91MA7 |
| F | Hemagglutinin HA2 | protein | 170 | 53% helix, 14% strand | Q91MA7 |
| G, H, J | 16.G.07 heavy chain | protein | 231 | 7% helix, 52% strand | — |
| I, K, L | 16.G.07 light chain | protein | 214 | 3% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains A, K, H, C, B, G, E, D, J, 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 | 535 | 0.84 | 0.90 | 36 | empty |
| 2 | 991 | 0.82 | 0.83 | 119 | empty |
| 3 | 874 | 0.79 | 0.82 | 99 | empty |
| 4 | 509 | 0.77 | 0.84 | 62 | empty |
| 5 | 136 | 0.76 | 0.95 | 27 | empty |
Interfaces
33 interfaces between chains.
- A–B · 3019 Ų buried · 44 hydrogen bonds · protein-protein
- E–F · 2992 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 2976 Ų buried · 43 hydrogen bonds · protein-protein
- H–L · 2103 Ų buried · 13 hydrogen bonds · protein-protein
- G–I · 2093 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide, 17 glycan (disulfide, N-glycosylation).
Compared structures
- 5KAN · Crystal structure of multidonor HV1-18-class broadly neutralizing Influenza A antibody… · the same entry in another collection · chain C against C, 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 Q91MA7
- Elsewhere: RCSB PDB 5KAN · PDBe 5KAN · UniProt Q91MA7
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