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Structure of influenza a neutralizing antibody selected from cultures of single human plasma cells in complex with human H3 influenza haemagglutinin.
Analyse Structure of influenza a neutralizing antibody selected from cultures of single… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZTJ
- Type
- protein
- Length
- 2,586 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain; FI6V3 antibody heavy chain; FI6V3…
- UniProt
- P03437
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 8 distinct chains · 11% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Hemagglutinin HA1 chain | protein | 318 | 9% helix, 39% strand | P03437 |
| B, D, F | Hemagglutinin HA2 chain | protein | 172 | 50% helix, 13% strand | P03437 |
| C | Hemagglutinin HA1 chain | protein | 316 | 10% helix, 37% strand | P03437 |
| G | FI6V3 antibody heavy chain | protein | 129 | 5% helix, 45% strand | — |
| H | FI6V3 antibody light chain | protein | 107 | 0% helix, 32% strand | — |
| I | FI6V3 antibody heavy chain | protein | 226 | 5% helix, 45% strand | — |
| J, L | FI6V3 antibody light chain | protein | 216 | 4% helix, 44% strand | — |
| K | FI6V3 antibody heavy chain | protein | 224 | 5% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 29 copies · chains A, G, E, B, C, I, K, F, D
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains E, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 840 | 0.86 | 0.89 | 132 | empty |
| 2 | 490 | 0.86 | 0.93 | 37 | empty |
| 3 | 259 | 0.85 | 0.97 | 29 | empty |
| 4 | 826 | 0.77 | 0.80 | 91 | empty |
| 5 | 318 | 0.76 | 0.88 | 53 | empty |
Interfaces
33 interfaces between chains.
- A–B · 2837 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 2833 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 2811 Ų buried · 39 hydrogen bonds · protein-protein
- K–L · 1828 Ų buried · 14 hydrogen bonds · protein-protein
- I–J · 1827 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 3ZTJ · Structure of influenza A neutralizing antibody selected from cultures of single human… · the same entry in another collection · chain E against E, 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 P03437
- Elsewhere: RCSB PDB 3ZTJ · PDBe 3ZTJ · UniProt P03437
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