MolNFT v1 · #82083 · protein
Crystal structure of formaldehyde treated empty human enterovirus 71 particle (cryo at 100K)
3VBO · Genome polyprotein, capsid protein VP1: “Crystal structure of formaldehyde treated empty human enterovirus 71 particle (cryo at 100K)”. X-ray diffraction, 1 ligand (NA), 7 pockets (best druggability 0.66). MolNFT v1 #82083 on…
- PDB
- 3VBO
- Type
- protein
- Length
- 694 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein, capsid protein VP1; Genome polyprotein, capsid protein VP2; Genome…
- UniProt
- B2ZUN0
- Ligands
- NA
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Genome polyprotein, capsid protein VP1 | protein | 218 | 9% helix, 34% strand | B2ZUN0 |
| B | Genome polyprotein, capsid protein VP2 | protein | 237 | 13% helix, 38% strand | B2ZUN0 |
| C | Genome polyprotein, capsid protein VP3 | protein | 239 | 12% helix, 33% strand | B2ZUN0 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 288 | 0.66 | 0.82 | 32 | empty |
| 2 | 240 | 0.52 | 0.76 | 36 | empty |
| 3 | 97 | 0.41 | 0.77 | 20 | empty |
| 4 | 79 | 0.41 | 0.79 | 16 | empty |
| 5 | 68 | 0.37 | 0.78 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 3080 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 1812 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 1563 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3VBO · Crystal structure of formaldehyde treated empty human Enterovirus 71 particle (cryo at… · 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 B2ZUN0
- Elsewhere: RCSB PDB 3VBO · PDBe 3VBO · UniProt B2ZUN0
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