Research workbench
Structural basis for immunization with post-fusion rsv F to elicit high neutralizing antibody titers
Analyse Structural basis for immunization with post-fusion rsv F to elicit high… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RKI
- Type
- protein
- Length
- 1,319 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fusion glycoprotein F0
- UniProt
- P03420
- Ligands
- NAG
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fusion glycoprotein F0 | protein | 441 | 40% helix, 30% strand | P03420 |
| B | Fusion glycoprotein F0 | protein | 439 | 40% helix, 30% strand | P03420 |
| C | Fusion glycoprotein F0 | protein | 439 | 38% helix, 30% strand | P03420 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.82 | 0.83 | 96 | empty |
| 2 | 927 | 0.78 | 0.80 | 117 | empty |
| 3 | 273 | 0.68 | 0.83 | 26 | empty |
| 4 | 199 | 0.58 | 0.81 | 43 | empty |
| 5 | 56 | 0.48 | 0.85 | 19 | empty |
Interfaces
3 interfaces between chains.
- B–C · 6302 Ų buried · 66 hydrogen bonds · protein-protein
- A–C · 6293 Ų buried · 69 hydrogen bonds · protein-protein
- A–B · 6225 Ų buried · 61 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 3RKI · Structural basis for immunization with post-fusion RSV F to elicit high neutralizing… · 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 P03420
- Elsewhere: RCSB PDB 3RKI · PDBe 3RKI · UniProt P03420
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