MolNFT v1 · #152548 · protein
Cryo-EM structure of echovirus 6 complexed with its attachment receptor CD55 at pH 7.4
6ILK · Capsid protein VP1: “Cryo-EM structure of echovirus 6 complexed with its attachment receptor CD55 at pH 7.4”. Electron microscopy, 1 ligand (SPH), 16 pockets (best druggability 0.80). MolNFT v1 #152548 on GenesisL1: 3D structure…
- PDB
- 6ILK
- Type
- protein
- Length
- 1,019 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1; Capsid protein VP2; Capsid protein VP3; Capsid protein VP4…
- UniProt
- P08174
- Ligands
- SPH
- Pockets
- 16 · best druggability 0.80
Structure
electron microscopy · 5 distinct chains · 7% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 278 | 8% helix, 30% strand | — |
| B | Capsid protein VP2 | protein | 252 | 9% helix, 36% strand | — |
| C | Capsid protein VP3 | protein | 238 | 9% helix, 27% strand | — |
| D | Capsid protein VP4 | protein | 59 | 5% helix, 15% strand | — |
| E | Complement decay-accelerating factor | protein | 192 | 0% helix, 38% 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
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 528 | 0.80 | 0.86 | 73 | SPH |
| 2 | 240 | 0.58 | 0.79 | 31 | empty |
| 3 | 101 | 0.54 | 0.84 | 21 | empty |
| 4 | 72 | 0.52 | 0.86 | 29 | empty |
| 5 | 145 | 0.49 | 0.78 | 21 | empty |
Interfaces
8 interfaces between chains.
- A–C · 4290 Ų buried · 52 hydrogen bonds · protein-protein
- A–B · 2125 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1606 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1207 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 942 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6ILK · Cryo-EM structure of Echovirus 6 complexed with its attachment receptor CD55 at PH 7.4 · the same entry in another collection · chain E against E, 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 0.90
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 6ILK · PDBe 6ILK · UniProt P08174
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