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Crystal structure of multidonor HV1-18-class broadly neutralizing influenza a antibody 16.A.26 in complex with A/HONG KONG/1-4-MA21- 1/1968 (H3N2) hemagglutinin
Analyse Crystal structure of multidonor HV1-18-class broadly neutralizing influenza a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K9Q
- Type
- protein
- Length
- 5,582 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1; Hemagglutinin HA2; 16.A.26 heavy chain; 16.A.26 light chain
- UniProt
- Q91MA7
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 13 distinct chains · 25% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin HA1 | protein | 320 | 10% helix, 41% strand | Q91MA7 |
| B | Hemagglutinin HA2 | protein | 168 | 55% helix, 14% strand | Q91MA7 |
| C | Hemagglutinin HA1 | protein | 319 | 10% helix, 41% strand | Q91MA7 |
| D | Hemagglutinin HA2 | protein | 169 | 54% helix, 14% strand | Q91MA7 |
| E, M, O | Hemagglutinin HA1 | protein | 318 | 10% helix, 41% strand | Q91MA7 |
| F | Hemagglutinin HA2 | protein | 168 | 55% helix, 14% strand | Q91MA7 |
| G, J, S, U, X | 16.A.26 heavy chain | protein | 231 | 7% helix, 49% strand | — |
| H | 16.A.26 heavy chain | protein | 228 | 8% helix, 50% strand | — |
| I, K, L, T, V, Y | 16.A.26 light chain | protein | 214 | 7% helix, 50% strand | — |
| N | Hemagglutinin HA2 | protein | 169 | 56% helix, 14% strand | Q91MA7 |
| P | Hemagglutinin HA2 | protein | 163 | 57% helix, 15% strand | Q91MA7 |
| Q | Hemagglutinin HA1 | protein | 318 | 9% helix, 42% strand | Q91MA7 |
| R | Hemagglutinin HA2 | protein | 167 | 55% helix, 14% strand | Q91MA7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 36 copies · chains A, B, H, M, C, Q, T, D, G, Y, E, F, J, N, S, L, O, P, U, R, X
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 | 719 | 0.85 | 0.88 | 93 | empty |
| 2 | 724 | 0.83 | 0.87 | 83 | empty |
| 3 | 611 | 0.83 | 0.88 | 87 | empty |
| 4 | 494 | 0.83 | 0.90 | 43 | empty |
| 5 | 677 | 0.82 | 0.86 | 56 | empty |
Interfaces
74 interfaces between chains.
- O–P · 2960 Ų buried · 47 hydrogen bonds · protein-protein
- Q–R · 2941 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 2903 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 2899 Ų buried · 39 hydrogen bonds · protein-protein
- E–F · 2891 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 65 disulfide, 36 glycan (disulfide, N-glycosylation).
Compared structures
- 5K9Q · Crystal structure of multidonor HV1-18-class broadly neutralizing Influenza A antibody… · 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 Q91MA7
- Elsewhere: RCSB PDB 5K9Q · PDBe 5K9Q · UniProt Q91MA7
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