Research workbench
Rsv prefusion F bound to RSD5 Fab
Analyse Rsv prefusion F bound to RSD5 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DC3
- Type
- protein
- Length
- 894 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab RSD5-germline heavy chain; Fab RSD5-germline light chain; Rsv fusion glycoprotein
- UniProt
- Q6N089, Q8N355, P03420, M1E1E4
- Ligands
- NAG, SO4
- Pockets
- 7 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fab RSD5-germline heavy chain | protein | 229 | 9% helix, 48% strand | Q6N089 |
| L | Fab RSD5-germline light chain | protein | 213 | 5% helix, 51% strand | Q8N355 |
| F | Rsv fusion glycoprotein | protein | 452 | 31% helix, 33% strand | P03420, M1E1E4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains F
- SO4 · Sulfate ion · ion · 13 copies · chains H, L, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 333 | 0.61 | 0.78 | 51 | empty |
| 2 | 459 | 0.58 | 0.74 | 50 | empty |
| 3 | 207 | 0.53 | 0.77 | 21 | empty |
| 4 | 117 | 0.46 | 0.79 | 20 | empty |
| 5 | 96 | 0.44 | 0.79 | 15 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1971 Ų buried · 20 hydrogen bonds · protein-protein
- H–F · 643 Ų buried · 8 hydrogen bonds · protein-protein
- L–F · 311 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6DC3 · RSV prefusion F bound to RSD5 Fab · the same entry in another collection · chain H against H, 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 Q6N089
- Every structure of UniProt Q8N355
- Every structure of UniProt P03420
- Every structure of UniProt M1E1E4
- Elsewhere: RCSB PDB 6DC3 · PDBe 6DC3 · UniProt Q6N089 · UniProt Q8N355 · UniProt P03420 · UniProt M1E1E4
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