MolNFT v1 · #135094 · protein
Crystal structure of the rsv F glycoprotein in complex with the neutralizing single-domain antibody F-vhh-L66
5TOK · Fusion glycoprotein F0, fibritin chimera: “Crystal structure of the rsv F glycoprotein in complex with the neutralizing single-domain antibody F-vhh-L66”. X-ray diffraction, 2 ligands (NAG, PO4), 20 pockets (best druggability 0.83).…
- PDB
- 5TOK
- Type
- protein
- Length
- 1,806 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fusion glycoprotein F0, fibritin chimera; Single-domain antibody F-vhh-L66
- UniProt
- P03420
- Ligands
- NAG, PO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Fusion glycoprotein F0, fibritin chimera | protein | 478 | 30% helix, 33% strand | P03420 |
| D, F | Single-domain antibody F-vhh-L66 | protein | 123 | 10% helix, 50% strand | — |
| E | Single-domain antibody F-vhh-L66 | protein | 126 | 10% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · chains A, 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 967 | 0.83 | 0.84 | 102 | empty |
| 2 | 574 | 0.81 | 0.87 | 53 | empty |
| 3 | 987 | 0.75 | 0.78 | 87 | empty |
| 4 | 521 | 0.74 | 0.82 | 69 | empty |
| 5 | 409 | 0.73 | 0.84 | 56 | empty |
Interfaces
9 interfaces between chains.
- A–C · 2921 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 2690 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2678 Ų buried · 29 hydrogen bonds · protein-protein
- A–E · 829 Ų buried · 12 hydrogen bonds · protein-protein
- C–F · 814 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5TOK · Crystal structure of the RSV F glycoprotein in complex with the 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 5TOK · PDBe 5TOK · UniProt P03420
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