Research workbench
Human rhinovirus 2 bound to a fragment of its cellular receptor protein
Analyse Human rhinovirus 2 bound to a fragment of its cellular receptor protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1V9U
- Type
- protein
- Length
- 820 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coat protein VP1; Coat protein VP2; Coat protein VP3; Coat protein VP4; LDL-receptor…
- UniProt
- P04936, P98155
- Ligands
- DAO, CA
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Coat protein VP1 | protein | 269 | 10% helix, 30% strand | P04936 |
| 2 | Coat protein VP2 | protein | 250 | 10% helix, 32% strand | P04936 |
| 3 | Coat protein VP3 | protein | 237 | 9% helix, 29% strand | P04936 |
| 4 | Coat protein VP4 | protein | 25 | 0% helix, 16% strand | P04936 |
| 5 | LDL-receptor class a 3 | protein | 39 | 15% helix, 0% strand | P98155 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 305 | 0.78 | 0.89 | 46 | DAO |
| 2 | 245 | 0.58 | 0.79 | 26 | empty |
| 3 | 252 | 0.53 | 0.76 | 41 | empty |
| 4 | 141 | 0.49 | 0.78 | 19 | empty |
| 5 | 105 | 0.46 | 0.79 | 28 | empty |
Interfaces
6 interfaces between chains.
- 1–3 · 4147 Ų buried · 59 hydrogen bonds · protein-protein
- 1–2 · 2138 Ų buried · 35 hydrogen bonds · protein-protein
- 2–3 · 1662 Ų buried · 19 hydrogen bonds · protein-protein
- 3–4 · 394 Ų buried · 6 hydrogen bonds · protein-protein
- 1–4 · 329 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1V9U · Human Rhinovirus 2 bound to a fragment of its cellular receptor protein · the same entry in another collection · chain 1 against 1, TM-score 1.00
- P98155 · AlphaFold monomer V2.0 prediction for very low-density lipoprotein receptor (P98155) · a predicted model of the same protein · chain 5 against A, TM-score 0.70
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 P04936
- Every structure of UniProt P98155
- Elsewhere: RCSB PDB 1V9U · PDBe 1V9U · UniProt P04936 · UniProt P98155
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