Research workbench
Cryo-EM structure of echovirus 11 complexed with its attaching receptor CD55 at pH 5.5
Analyse Cryo-EM structure of echovirus 11 complexed with its attaching receptor CD55 at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LAO
- Type
- protein
- Length
- 833 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.64
- Source
- Echovirus E11
- Molecule
- Capsid protein VP1; Capsid protein VP2; Capsid protein VP3; Capsid protein VP4
- Ligands
- SPH
- Pockets
- 13 · best druggability 0.78
Structure
electron microscopy · resolution 2.64 · 4 distinct chains · 9% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 285 | 9% helix, 32% strand | — |
| B | Capsid protein VP2 | protein | 251 | 10% helix, 38% strand | — |
| C | Capsid protein VP3 | protein | 238 | 8% helix, 30% strand | — |
| D | Capsid protein VP4 | protein | 59 | 12% helix, 17% strand | — |
Ligands and binding sites
- SPH · Sphingosine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 602 | 0.78 | 0.84 | 83 | SPH |
| 2 | 50 | 0.70 | 0.98 | 16 | empty |
| 3 | 78 | 0.53 | 0.86 | 28 | empty |
| 4 | 129 | 0.52 | 0.81 | 30 | empty |
| 5 | 178 | 0.51 | 0.78 | 28 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4470 Ų buried · 57 hydrogen bonds · protein-protein
- A–B · 2100 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1553 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1485 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 924 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6LAO · Cryo-EM structure of echovirus 11 complexed with its attaching receptor CD55 at pH 5.5 · 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
- Elsewhere: RCSB PDB 6LAO · PDBe 6LAO
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