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Cryoem structure of rhinovirus B14 in complex with C5 Fab (33 degrees celsius, molar ratio 1:3, full 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
- 5W3E
- Type
- protein
- Length
- 1,028 residues
- Chains
- 6
- 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
- 17 · best druggability 0.79
Structure
electron microscopy · 6 distinct chains · 9% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | C5 antibody variable heavy domain | protein | 116 | 5% helix, 49% strand | — |
| G | C5 antibody variable light domain | protein | 107 | 3% helix, 48% strand | — |
| A | Viral protein 1 | protein | 274 | 9% helix, 31% strand | P03303 |
| B | Viral protein 3 | protein | 236 | 7% helix, 32% strand | P03303 |
| C | Viral protein 2 | protein | 255 | 14% helix, 36% strand | P03303 |
| D | Viral protein 4 | protein | 40 | 18% helix, 3% strand | P03303 |
Pockets
17 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 167 | 0.79 | 0.95 | 34 | empty |
| 2 | 106 | 0.69 | 0.91 | 24 | empty |
| 3 | 365 | 0.67 | 0.81 | 49 | empty |
| 4 | 118 | 0.45 | 0.78 | 23 | empty |
| 5 | 99 | 0.39 | 0.76 | 22 | empty |
Interfaces
12 interfaces between chains.
- A–B · 4154 Ų buried · 75 hydrogen bonds · protein-protein
- A–C · 2133 Ų buried · 48 hydrogen bonds · protein-protein
- B–C · 1703 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 924 Ų buried · 18 hydrogen bonds · protein-protein
- E–G · 882 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5W3E · CryoEM structure of rhinovirus B14 in complex with C5 Fab (33 degrees Celsius, molar… · the same entry in another collection · chain G against G, 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 5W3E · PDBe 5W3E · UniProt P03303
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