MolNFT v1 · #135093 · protein
Crystal structure of the rsv F glycoprotein in complex with the neutralizing single-domain antibody F-vhh-4
5TOJ · Fusion glycoprotein F0, fibritin chimera: “Crystal structure of the rsv F glycoprotein in complex with the neutralizing single-domain antibody F-vhh-4”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.83). MolNFT…
- PDB
- 5TOJ
- Type
- protein
- Length
- 1,823 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-4
- UniProt
- P03420
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 27% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fusion glycoprotein F0, fibritin chimera | protein | 483 | 30% helix, 33% strand | P03420 |
| B | Fusion glycoprotein F0, fibritin chimera | protein | 485 | 31% helix, 33% strand | P03420 |
| C | Fusion glycoprotein F0, fibritin chimera | protein | 481 | 31% helix, 32% strand | P03420 |
| D | Single-domain antibody F-vhh-4 | protein | 126 | 10% helix, 48% strand | — |
| E | Single-domain antibody F-vhh-4 | protein | 123 | 10% helix, 48% strand | — |
| F | Single-domain antibody F-vhh-4 | protein | 125 | 10% helix, 49% 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
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 754 | 0.83 | 0.87 | 63 | empty |
| 2 | 869 | 0.79 | 0.82 | 67 | empty |
| 3 | 143 | 0.78 | 0.95 | 33 | empty |
| 4 | 238 | 0.77 | 0.91 | 38 | empty |
| 5 | 248 | 0.75 | 0.89 | 36 | empty |
Interfaces
9 interfaces between chains.
- A–C · 3001 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 2950 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2869 Ų buried · 29 hydrogen bonds · protein-protein
- B–E · 796 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 793 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5TOJ · 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 5TOJ · PDBe 5TOJ · UniProt P03420
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