Research workbench
Structure of echovirus 18 in complex with neonatal Fc receptor
Analyse Structure of echovirus 18 in complex with neonatal Fc receptor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B5F
- Type
- protein
- Length
- 958 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Echovirus 18 viral protein 3; Echovirus 18 viral protein 4; Echovirus 18 viral protein 1…
- EC
- 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48
- UniProt
- Q8V635, P55899, P61769
- Ligands
- PLM, GUN
- Pockets
- 10 · best druggability 0.79
Structure
electron microscopy · 6 distinct chains · 12% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Echovirus 18 viral protein 3 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 239 | 9% helix, 31% strand | Q8V635 |
| D | Echovirus 18 viral protein 4 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 40 | 10% helix, 3% strand | Q8V635 |
| A | Echovirus 18 viral protein 1 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 269 | 8% helix, 29% strand | Q8V635 |
| B | Echovirus 18 viral protein 2 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 249 | 11% helix, 39% strand | Q8V635 |
| G | IgG receptor fcrn large subunit P51 | protein | 133 | 33% helix, 37% strand | P55899 |
| H | Beta-2-microglobulin | protein | 28 | 0% helix, 32% strand | P61769 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 639 | 0.79 | 0.84 | 88 | PLM |
| 2 | 85 | 0.74 | 0.97 | 23 | empty |
| 3 | 138 | 0.48 | 0.78 | 28 | empty |
| 4 | 137 | 0.44 | 0.76 | 29 | empty |
| 5 | 108 | 0.43 | 0.78 | 27 | empty |
Interfaces
10 interfaces between chains.
- C–A · 4358 Ų buried · 71 hydrogen bonds · protein-protein
- A–B · 2022 Ų buried · 34 hydrogen bonds · protein-protein
- C–B · 1595 Ų buried · 19 hydrogen bonds · protein-protein
- D–A · 1098 Ų buried · 16 hydrogen bonds · protein-protein
- A–G · 983 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7B5F · Structure of echovirus 18 in complex with neonatal Fc receptor · the same entry in another collection · chain H against H, TM-score 1.00
- P55899 · AlphaFold monomer V2.0 prediction for IgG receptor fcrn large subunit P51 (P55899) · a predicted model of the same protein · chain G against A, TM-score 0.98
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain H against A, TM-score 0.86
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 Q8V635
- Every structure of UniProt P55899
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 7B5F · PDBe 7B5F · UniProt Q8V635 · UniProt P55899 · UniProt P61769
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