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Structure of the niv F glycoprotein in complex with the 12B2 neutralizing antibody
Analyse Structure of the niv F glycoprotein in complex with the 12B2 neutralizing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KI4
- Type
- protein
- Length
- 2,010 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fusion glycoprotein F0; 12B2 Fab light chain; 12B2 heavy chain
- UniProt
- Q9IH63
- Ligands
- NAG, BMA, MAN, FUC
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 3 distinct chains · 26% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Fusion glycoprotein F0 | protein | 448 | 37% helix, 29% strand | Q9IH63 |
| L, C, F | 12B2 Fab light chain | protein | 105 | 3% helix, 48% strand | — |
| H, D, G | 12B2 heavy chain | protein | 117 | 3% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, B, E, H, L, D, C, G, F
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains H, D, G
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains L, H, C, D, F, G
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, F, L, B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1076 | 0.81 | 0.82 | 62 | empty |
| 2 | 583 | 0.73 | 0.81 | 54 | NAG |
| 3 | 802 | 0.70 | 0.76 | 86 | empty |
| 4 | 756 | 0.66 | 0.74 | 65 | empty |
| 5 | 287 | 0.62 | 0.80 | 42 | empty |
Interfaces
18 interfaces between chains.
- A–B · 2985 Ų buried · 34 hydrogen bonds · protein-protein
- B–E · 2977 Ų buried · 34 hydrogen bonds · protein-protein
- A–E · 2969 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 851 Ų buried · 5 hydrogen bonds · protein-protein
- F–G · 851 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 7KI4 · Structure of the NiV F glycoprotein in complex with the 12B2 neutralizing 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 Q9IH63
- Elsewhere: RCSB PDB 7KI4 · PDBe 7KI4 · UniProt Q9IH63
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