MolNFT v1 · #63862 · protein
Structure of rotavirus outer capsid protein VP7 trimer in complex with a neutralizing Fab
3FMG · Fab of neutralizing antibody 4F8, light chain: “Structure of rotavirus outer capsid protein VP7 trimer in complex with a neutralizing Fab”. X-ray diffraction, 1 ligand (CA), 9 pockets (best druggability 0.49). MolNFT v1 #63862 on…
- PDB
- 3FMG
- Type
- protein
- Length
- 667 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab of neutralizing antibody 4F8, light chain; Fab of neutralizing antibody 4F8, heavy…
- UniProt
- P12476
- Ligands
- CA
- Pockets
- 9 · best druggability 0.49
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Fab of neutralizing antibody 4F8, light chain | protein | 211 | 6% helix, 43% strand | — |
| H | Fab of neutralizing antibody 4F8, heavy chain | protein | 221 | 1% helix, 48% strand | — |
| A | Glycoprotein VP7 | protein | 235 | 23% helix, 35% strand | P12476 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 207 | 0.49 | 0.76 | 33 | empty |
| 2 | 251 | 0.48 | 0.74 | 39 | empty |
| 3 | 63 | 0.46 | 0.83 | 16 | empty |
| 4 | 148 | 0.44 | 0.76 | 26 | empty |
| 5 | 147 | 0.41 | 0.74 | 30 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1821 Ų buried · 18 hydrogen bonds · protein-protein
- H–A · 271 Ų buried · 6 hydrogen bonds · protein-protein
- L–A · 89 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3FMG · Structure of rotavirus outer capsid protein VP7 trimer in complex with a neutralizing Fab · the same entry in another collection · chain L against L, 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 P12476
- Elsewhere: RCSB PDB 3FMG · PDBe 3FMG · UniProt P12476
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