Research workbench
Crystal structure of non-neutralizing infant antibody adi-14359 in complex with postfusion rsv F glycoprotein
Analyse Crystal structure of non-neutralizing infant antibody adi-14359 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6APB
- Type
- protein
- Length
- 1,713 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fusion glycoprotein F0,FUSION glycoprotein F0; IgG H chain; Adi-14359 Fab light chain
- UniProt
- Q84850, A0A1P8J9V4
- Ligands
- NAG
- Pockets
- 17 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 31% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fusion glycoprotein F0,FUSION glycoprotein F0 | protein | 428 | 39% helix, 31% strand | Q84850, A0A1P8J9V4 |
| B | Fusion glycoprotein F0,FUSION glycoprotein F0 | protein | 429 | 39% helix, 31% strand | Q84850, A0A1P8J9V4 |
| C | Fusion glycoprotein F0,FUSION glycoprotein F0 | protein | 425 | 40% helix, 31% strand | Q84850, A0A1P8J9V4 |
| H | IgG H chain | protein | 219 | 5% helix, 53% strand | — |
| L | Adi-14359 Fab light chain | protein | 212 | 4% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 448 | 0.84 | 0.91 | 38 | empty |
| 2 | 1065 | 0.83 | 0.84 | 145 | empty |
| 3 | 175 | 0.71 | 0.89 | 25 | empty |
| 4 | 527 | 0.61 | 0.74 | 54 | empty |
| 5 | 127 | 0.57 | 0.83 | 20 | empty |
Interfaces
7 interfaces between chains.
- B–C · 6096 Ų buried · 60 hydrogen bonds · protein-protein
- A–B · 6000 Ų buried · 57 hydrogen bonds · protein-protein
- A–C · 5997 Ų buried · 60 hydrogen bonds · protein-protein
- H–L · 1889 Ų buried · 15 hydrogen bonds · protein-protein
- C–H · 544 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 25 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6APB · Crystal Structure of Non-Neutralizing Infant Antibody ADI-14359 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 Q84850
- Every structure of UniProt A0A1P8J9V4
- Elsewhere: RCSB PDB 6APB · PDBe 6APB · UniProt Q84850 · UniProt A0A1P8J9V4
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