Research workbench
Structure of rsv F in complex with vhh CL184
Analyse Structure of rsv F in complex with vhh CL184 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LVW
- Type
- protein
- Length
- 3,670 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fusion glycoprotein F0; F-vhh-CL184
- UniProt
- W8RJF9
- Ligands
- NAG, BMA, CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 28% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Fusion glycoprotein F0 | protein | 489 | 31% helix, 33% strand | W8RJF9 |
| G, I, L, J, H | F-vhh-CL184 | protein | 123 | 7% helix, 48% strand | — |
| B, E | Fusion glycoprotein F0 | protein | 488 | 32% helix, 32% strand | W8RJF9 |
| F | Fusion glycoprotein F0 | protein | 491 | 32% helix, 33% strand | W8RJF9 |
| K | F-vhh-CL184 | protein | 121 | 5% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains D, A, F
- BMA · beta-D-mannopyranose · sugar
- CL · Chloride ion · ion · 5 copies · chains A, D, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1102 | 0.83 | 0.85 | 74 | empty |
| 2 | 1129 | 0.83 | 0.84 | 79 | empty |
| 3 | 1118 | 0.81 | 0.83 | 106 | empty |
| 4 | 674 | 0.76 | 0.82 | 54 | empty |
| 5 | 911 | 0.75 | 0.78 | 83 | empty |
Interfaces
17 interfaces between chains.
- C–F · 3179 Ų buried · 39 hydrogen bonds · protein-protein
- E–F · 3064 Ų buried · 34 hydrogen bonds · protein-protein
- B–D · 3048 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 2961 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 2919 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 7LVW · Structure of RSV F in Complex with VHH Cl184 · 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 W8RJF9
- Elsewhere: RCSB PDB 7LVW · PDBe 7LVW · UniProt W8RJF9
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