Research workbench
Complex of echovirus type 12 with domains 3 and 4 of its receptor decay accelerating factor (CD55) by cryo electron microscopy at 16 a
Analyse Complex of echovirus type 12 with domains 3 and 4 of its receptor decay… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UPN
- Type
- protein
- Length
- 964 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Echovirus 11 coat protein VP1; Echovirus 11 coat protein VP2; Echovirus 11 coat protein…
- UniProt
- Q8JKE8, P08174
- Pockets
- 12 · best druggability 0.78
Structure
electron microscopy · 5 distinct chains · 9% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Echovirus 11 coat protein VP1 | protein | 289 | 11% helix, 30% strand | Q8JKE8 |
| B | Echovirus 11 coat protein VP2 | protein | 252 | 10% helix, 38% strand | Q8JKE8 |
| C | Echovirus 11 coat protein VP3 | protein | 238 | 10% helix, 33% strand | Q8JKE8 |
| D | Echovirus 11 coat protein VP4 | protein | 60 | 10% helix, 17% strand | Q8JKE8 |
| E | Complement decay-accelerating factor | protein | 125 | 0% helix, 46% strand | P08174 |
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 | 465 | 0.78 | 0.85 | 60 | empty |
| 2 | 405 | 0.67 | 0.80 | 62 | empty |
| 3 | 75 | 0.61 | 0.90 | 15 | empty |
| 4 | 61 | 0.55 | 0.89 | 23 | empty |
| 5 | 298 | 0.54 | 0.75 | 27 | empty |
Interfaces
9 interfaces between chains.
- A–C · 4466 Ų buried · 78 hydrogen bonds · protein-protein
- A–B · 1982 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1626 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1478 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 947 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1UPN · Complex of echovirus type 12 with domains 3 and 4 of its receptor decay accelerating… · 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 0.86
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 Q8JKE8
- Every structure of UniProt P08174
- Elsewhere: RCSB PDB 1UPN · PDBe 1UPN · UniProt Q8JKE8 · UniProt P08174
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