MolNFT v1 · #125014 · protein
Structural basis for norovirus neutralization by a hbga blocking human IgA antibody
5KW9 · Capsid protein VP1: “Structural basis for norovirus neutralization by a hbga blocking human IgA antibody”. X-ray diffraction, 2 ligands (MG, NA), 5 pockets (best druggability 0.57). MolNFT v1 #125014 on GenesisL1: 3D structure…
- PDB
- 5KW9
- Type
- protein
- Length
- 723 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1; IGA(VH)-IGG(CH) heavy chain Fab fragment; IgA light chain
- UniProt
- Q83884
- Ligands
- MG, NA
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 289 | 9% helix, 31% strand | Q83884 |
| H | IGA(VH)-IGG(CH) heavy chain Fab fragment | protein | 215 | 9% helix, 51% strand | — |
| L | IgA light chain | protein | 219 | 6% helix, 52% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 5 copies · chains A, H, L
- NA · Sodium ion · metal · 3 copies · chains A, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 412 | 0.57 | 0.74 | 55 | empty |
| 2 | 222 | 0.55 | 0.78 | 44 | empty |
| 3 | 141 | 0.43 | 0.76 | 30 | empty |
| 4 | 103 | 0.37 | 0.75 | 24 | empty |
| 5 | 50 | 0.23 | 0.72 | 18 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1705 Ų buried · 14 hydrogen bonds · protein-protein
- A–L · 644 Ų buried · 12 hydrogen bonds · protein-protein
- A–H · 189 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5KW9 · Structural Basis for Norovirus Neutralization by a HBGA Blocking Human IgA 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 Q83884
- Elsewhere: RCSB PDB 5KW9 · PDBe 5KW9 · UniProt Q83884
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