Research workbench
Cryoem structure of foot and mouth disease virus O panasia
Analyse Cryoem structure of foot and mouth disease virus O panasia in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NED
- Type
- protein
- Length
- 656 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O panasia VP1; O panasia VP2; O panasia VP3; O panasia VP4
- UniProt
- A0A1B0SZV3, A0A1B0QWS1, J3T9N5, E6Y5R5
- Pockets
- 6 · best druggability 0.72
Structure
electron microscopy · 4 distinct chains · 10% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | O panasia VP1 | protein | 184 | 11% helix, 28% strand | A0A1B0SZV3 |
| B | O panasia VP2 | protein | 206 | 8% helix, 43% strand | A0A1B0QWS1 |
| C | O panasia VP3 | protein | 220 | 8% helix, 33% strand | J3T9N5 |
| D | O panasia VP4 | protein | 46 | 22% helix, 2% strand | E6Y5R5 |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 657 | 0.72 | 0.79 | 62 | empty |
| 2 | 588 | 0.70 | 0.79 | 63 | empty |
| 3 | 423 | 0.66 | 0.79 | 46 | empty |
| 4 | 143 | 0.44 | 0.76 | 20 | empty |
| 5 | 100 | 0.41 | 0.77 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1293 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1075 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 898 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 824 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 248 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5NED · CryoEM Structure of Foot and Mouth Disease Virus O PanAsia · 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 A0A1B0SZV3
- Every structure of UniProt A0A1B0QWS1
- Every structure of UniProt J3T9N5
- Every structure of UniProt E6Y5R5
- Elsewhere: RCSB PDB 5NED · PDBe 5NED · UniProt A0A1B0SZV3 · UniProt A0A1B0QWS1 · UniProt J3T9N5 · UniProt E6Y5R5
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