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Cryoem structure of rhinovirus B14 in complex with C5 Fab (4 degrees celsius, molar ratio 1:3, full particle)
Analyse Cryoem structure of rhinovirus B14 in complex with C5 Fab (4 degrees celsius… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W3L
- Type
- protein
- Length
- 1,028 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Viral protein 1; Viral protein 3; Viral protein 2; Viral protein 4; C5 antibody variable…
- UniProt
- P03303
- Pockets
- 15 · best druggability 0.77
Structure
electron microscopy · 6 distinct chains · 7% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Viral protein 1 | protein | 274 | 8% helix, 32% strand | P03303 |
| B | Viral protein 3 | protein | 236 | 7% helix, 32% strand | P03303 |
| C | Viral protein 2 | protein | 255 | 13% helix, 35% strand | P03303 |
| D | Viral protein 4 | protein | 40 | 10% helix, 3% strand | P03303 |
| E | C5 antibody variable heavy domain | protein | 116 | 3% helix, 52% strand | — |
| G | C5 antibody variable light domain | protein | 107 | 0% helix, 49% strand | — |
Pockets
15 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 507 | 0.77 | 0.84 | 70 | empty |
| 2 | 99 | 0.75 | 0.96 | 34 | empty |
| 3 | 95 | 0.42 | 0.78 | 22 | empty |
| 4 | 103 | 0.42 | 0.77 | 25 | empty |
| 5 | 62 | 0.40 | 0.80 | 21 | empty |
Interfaces
12 interfaces between chains.
- A–B · 4147 Ų buried · 80 hydrogen bonds · protein-protein
- A–C · 2143 Ų buried · 51 hydrogen bonds · protein-protein
- B–C · 1686 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 966 Ų buried · 11 hydrogen bonds · protein-protein
- E–G · 927 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5W3L · CryoEM structure of rhinovirus B14 in complex with C5 Fab (4 degrees Celsius, molar ratio… · 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 P03303
- Elsewhere: RCSB PDB 5W3L · PDBe 5W3L · UniProt P03303
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