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Cryoem structure of rhinovirus B14 in complex with C5 Fab (33 degrees celsius, molar ratio 1:3, empty particle)
Analyse Cryoem structure of rhinovirus B14 in complex with C5 Fab (33 degrees celsius… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W3O
- Type
- protein
- Length
- 901 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C5 antibody variable heavy domain; C5 antibody variable light domain; Viral protein 1…
- UniProt
- P03303
- Pockets
- 12 · best druggability 0.76
Structure
electron microscopy · 5 distinct chains · 8% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | C5 antibody variable heavy domain | protein | 116 | 3% helix, 43% strand | — |
| E | C5 antibody variable light domain | protein | 107 | 0% helix, 45% strand | — |
| A | Viral protein 1 | protein | 229 | 9% helix, 32% strand | P03303 |
| B | Viral protein 3 | protein | 215 | 9% helix, 32% strand | P03303 |
| C | Viral protein 2 | protein | 234 | 12% helix, 34% strand | P03303 |
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 105 | 0.76 | 0.97 | 26 | empty |
| 2 | 189 | 0.72 | 0.89 | 24 | empty |
| 3 | 388 | 0.67 | 0.80 | 47 | empty |
| 4 | 132 | 0.47 | 0.78 | 27 | empty |
| 5 | 118 | 0.45 | 0.78 | 20 | empty |
Interfaces
9 interfaces between chains.
- A–B · 2812 Ų buried · 50 hydrogen bonds · protein-protein
- A–C · 1750 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 1472 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 877 Ų buried · 6 hydrogen bonds · protein-protein
- E–B · 421 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5W3O · CryoEM structure of rhinovirus B14 in complex with C5 Fab (33 degrees Celsius, molar… · the same entry in another collection · chain D against D, 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 P03303
- Elsewhere: RCSB PDB 5W3O · PDBe 5W3O · UniProt P03303
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