Research workbench
Cryo-EM structure of echovirus 11 complexed with its attaching receptor CD55 at pH 7.4
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
- 6LA5
- Type
- protein
- Length
- 958 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.86
- Source
- Echovirus E11; Homo sapiens
- Molecule
- Capsid protein VP1; Capsid protein VP2; Capsid protein VP3; Capsid protein VP4…
- UniProt
- P08174
- Ligands
- SPH
- Pockets
- 12 · best druggability 0.82
Structure
electron microscopy · resolution 2.86 · 5 distinct chains · 6% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 285 | 9% helix, 31% strand | — |
| B | Capsid protein VP2 | protein | 251 | 6% helix, 37% strand | — |
| C | Capsid protein VP3 | protein | 238 | 6% helix, 29% strand | — |
| D | Capsid protein VP4 | protein | 59 | 10% helix, 17% strand | — |
| E | Complement decay-accelerating factor | protein | 125 | 0% helix, 46% strand | P08174 |
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
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 247 | 0.82 | 0.94 | 35 | SPH |
| 2 | 746 | 0.72 | 0.78 | 94 | empty |
| 3 | 69 | 0.52 | 0.86 | 24 | empty |
| 4 | 148 | 0.50 | 0.79 | 22 | empty |
| 5 | 250 | 0.50 | 0.75 | 37 | empty |
Interfaces
9 interfaces between chains.
- A–C · 4456 Ų buried · 66 hydrogen bonds · protein-protein
- A–B · 2035 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1580 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1540 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 942 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6LA5 · Cryo-EM structure of echovirus 11 complexed with its attaching receptor CD55 at pH 7.4 · 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 0.95
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 6LA5 · PDBe 6LA5 · UniProt P08174
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