MolNFT v1 · #61579 · protein
Human rhinovirus 2 bound to a concatamer of the vldl receptor module V3
3DPR · Protein VP1: “Human rhinovirus 2 bound to a concatamer of the vldl receptor module V3”. X-ray diffraction, 2 ligands (DAO, CA), 11 pockets (best druggability 0.80). MolNFT v1 #61579 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3DPR
- Type
- protein
- Length
- 820 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein VP1; Protein VP2; Protein VP3; Protein VP4; LDL-receptor class a 3
- UniProt
- P04936, P98155
- Ligands
- DAO, CA
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein VP1 | protein | 269 | 9% helix, 30% strand | P04936 |
| B | Protein VP2 | protein | 250 | 12% helix, 35% strand | P04936 |
| C | Protein VP3 | protein | 237 | 8% helix, 32% strand | P04936 |
| D | Protein VP4 | protein | 25 | 12% helix, 16% strand | P04936 |
| E | LDL-receptor class a 3 | protein | 39 | 0% 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 | 230 | 0.80 | 0.93 | 38 | DAO |
| 2 | 207 | 0.54 | 0.78 | 22 | empty |
| 3 | 234 | 0.52 | 0.76 | 43 | empty |
| 4 | 199 | 0.47 | 0.75 | 30 | empty |
| 5 | 119 | 0.47 | 0.79 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4195 Ų buried · 71 hydrogen bonds · protein-protein
- A–B · 2137 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 1710 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 379 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 333 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3DPR · Human rhinovirus 2 bound to a concatamer of the VLDL receptor module V3 · the same entry in another collection · chain A against A, 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 E 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 3DPR · PDBe 3DPR · UniProt P04936 · UniProt P98155
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