MolNFT v1 · #176515 · protein
Cryo-EM structure of coxsackievirus B1 mature virion
7DPF · Virion protein 1: “Cryo-EM structure of coxsackievirus B1 mature virion”. Electron microscopy, 1 ligand (PLM), 13 pockets (best druggability 0.79). MolNFT v1 #176515 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7DPF
- Type
- protein
- Length
- 810 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Virion protein 1; VP2; VP3; Capsid protein VP4
- UniProt
- W8GTF7, A0A2S0RQC2, A0A0G4PYT0, A0A2S1FMR1
- Ligands
- PLM
- Pockets
- 13 · best druggability 0.79
Structure
electron microscopy · 4 distinct chains · 9% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Virion protein 1 | protein | 267 | 9% helix, 32% strand | W8GTF7 |
| 2 | VP2 | protein | 252 | 10% helix, 35% strand | A0A2S0RQC2 |
| 3 | VP3 | protein | 237 | 8% helix, 27% strand | A0A0G4PYT0 |
| 4 | Capsid protein VP4 | protein | 54 | 13% helix, 13% strand | A0A2S1FMR1 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · chains 1
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 607 | 0.79 | 0.84 | 81 | PLM |
| 2 | 131 | 0.54 | 0.81 | 26 | empty |
| 3 | 170 | 0.52 | 0.79 | 27 | empty |
| 4 | 75 | 0.50 | 0.84 | 21 | empty |
| 5 | 125 | 0.45 | 0.77 | 22 | empty |
Interfaces
6 interfaces between chains.
- 1–3 · 4147 Ų buried · 49 hydrogen bonds · protein-protein
- 1–2 · 2112 Ų buried · 22 hydrogen bonds · protein-protein
- 2–3 · 1582 Ų buried · 12 hydrogen bonds · protein-protein
- 1–4 · 1090 Ų buried · 9 hydrogen bonds · protein-protein
- 3–4 · 847 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7DPF · Cryo-EM structure of Coxsackievirus B1 mature virion · the same entry in another collection · chain 1 against 1, 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 W8GTF7
- Every structure of UniProt A0A2S0RQC2
- Every structure of UniProt A0A0G4PYT0
- Every structure of UniProt A0A2S1FMR1
- Elsewhere: RCSB PDB 7DPF · PDBe 7DPF · UniProt W8GTF7 · UniProt A0A2S0RQC2 · UniProt A0A0G4PYT0 · UniProt A0A2S1FMR1
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