Research workbench
Crystal structure of broadly neutralizing influenza a antibody 31.A.83 in complex with hemagglutinin hong kong 1968.
Analyse Crystal structure of broadly neutralizing influenza a antibody 31.A.83 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KAQ
- Type
- protein
- Length
- 2,780 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Antibody 31.A.83 Fab heavy chain; Antibody 31.A.83 Fab light chain
- UniProt
- E1AFM4
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 18% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 481 | 24% helix, 30% strand | E1AFM4 |
| C | Hemagglutinin | protein | 482 | 25% helix, 29% strand | E1AFM4 |
| F | Antibody 31.A.83 Fab heavy chain | protein | 232 | 5% helix, 42% strand | — |
| G, L, R | Antibody 31.A.83 Fab light chain | protein | 213 | 5% helix, 44% strand | — |
| B | Hemagglutinin | protein | 480 | 25% helix, 30% strand | E1AFM4 |
| H, Q | Antibody 31.A.83 Fab heavy chain | protein | 233 | 4% helix, 43% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, Q, B, C, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 711 | 0.81 | 0.85 | 36 | empty |
| 2 | 1057 | 0.81 | 0.82 | 118 | empty |
| 3 | 833 | 0.80 | 0.83 | 83 | empty |
| 4 | 1175 | 0.75 | 0.77 | 119 | empty |
| 5 | 976 | 0.74 | 0.77 | 88 | empty |
Interfaces
18 interfaces between chains.
- Q–R · 2167 Ų buried · 18 hydrogen bonds · protein-protein
- C–B · 2130 Ų buried · 25 hydrogen bonds · protein-protein
- H–L · 2118 Ų buried · 19 hydrogen bonds · protein-protein
- F–G · 2097 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2060 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 33 disulfide, 17 glycan (disulfide, N-glycosylation).
Compared structures
- 5KAQ · Crystal structure of broadly neutralizing Influenza A antibody 31.a.83 in complex with… · 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 E1AFM4
- Elsewhere: RCSB PDB 5KAQ · PDBe 5KAQ · UniProt E1AFM4
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