MolNFT v1 · #189829 · protein
Coxsackievirus B3(VP3-234N) incubate with CD55 at PH7.4
7VY6 · Capsid protein VP1: “Coxsackievirus B3(VP3-234N) incubate with CD55 at PH7.4”. Electron microscopy, 1 ligand (PLM), 11 pockets (best druggability 0.79). MolNFT v1 #189829 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7VY6
- Type
- protein
- Length
- 939 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1; Capsid protein VP2; Capsid protein VP3; Capsid protein VP4…
- UniProt
- P08174
- Ligands
- PLM
- Pockets
- 11 · best druggability 0.79
Structure
electron microscopy · 5 distinct chains · 8% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 268 | 8% helix, 31% strand | — |
| B | Capsid protein VP2 | protein | 255 | 9% helix, 38% strand | — |
| C | Capsid protein VP3 | protein | 238 | 11% helix, 29% strand | — |
| D | Capsid protein VP4 | protein | 57 | 0% helix, 12% strand | — |
| E | Complement decay-accelerating factor | protein | 121 | 2% helix, 32% strand | P08174 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 613 | 0.79 | 0.84 | 84 | PLM |
| 2 | 544 | 0.70 | 0.79 | 75 | empty |
| 3 | 167 | 0.49 | 0.77 | 23 | empty |
| 4 | 137 | 0.48 | 0.78 | 28 | empty |
| 5 | 84 | 0.44 | 0.80 | 23 | empty |
Interfaces
9 interfaces between chains.
- A–C · 4331 Ų buried · 54 hydrogen bonds · protein-protein
- A–B · 2110 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1599 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1143 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 918 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7VY6 · Coxsackievirus B3(VP3-234N) incubate with CD55 at pH7.4 · the same entry in another collection · chain A against A, TM-score 1.00
- P08174 · AlphaFold monomer V2.0 prediction for complement decay-accelerating factor (P08174) · a predicted model of the same protein · chain E against A, TM-score 0.90
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 P08174
- Elsewhere: RCSB PDB 7VY6 · PDBe 7VY6 · UniProt P08174
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.