Research workbench
Structure of the hev F glycoprotein in complex with the 1F5 neutralizing antibody
Analyse Structure of the hev F glycoprotein in complex with the 1F5 neutralizing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KI6
- Type
- protein
- Length
- 1,986 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fusion glycoprotein F0; 1F5 Fab light chain; 1F5 heavy chain
- UniProt
- F4YH70
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 3 distinct chains · 25% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Fusion glycoprotein F0 | protein | 437 | 36% helix, 30% strand | F4YH70 |
| L, C, F | 1F5 Fab light chain | protein | 108 | 3% helix, 52% strand | — |
| H, D, G | 1F5 heavy chain | protein | 117 | 8% helix, 53% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, E, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.79 | 0.80 | 59 | empty |
| 2 | 847 | 0.77 | 0.81 | 92 | empty |
| 3 | 777 | 0.76 | 0.81 | 80 | empty |
| 4 | 795 | 0.76 | 0.80 | 80 | empty |
| 5 | 601 | 0.73 | 0.81 | 79 | empty |
Interfaces
15 interfaces between chains.
- A–E · 2846 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 2841 Ų buried · 37 hydrogen bonds · protein-protein
- B–E · 2838 Ų buried · 37 hydrogen bonds · protein-protein
- L–H · 893 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 889 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 7KI6 · Structure of the HeV F glycoprotein in complex with the 1F5 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 F4YH70
- Elsewhere: RCSB PDB 7KI6 · PDBe 7KI6 · UniProt F4YH70
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