Research workbench
The interaction of decay-accelerating factor with echovirus 7
Analyse The interaction of decay-accelerating factor with echovirus 7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IYP
- Type
- protein
- Length
- 1,080 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein; Polyprotein; Complement decay-accelerating factor
- UniProt
- Q9QP24, Q6W9E5, Q91QV1, P08174
- Ligands
- DAO
- Pockets
- 16 · best druggability 0.80
Structure
electron microscopy · 5 distinct chains · 8% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein | protein | 277 | 9% helix, 32% strand | Q9QP24 |
| B | Polyprotein | protein | 238 | 9% helix, 28% strand | Q6W9E5 |
| C | Polyprotein | protein | 252 | 11% helix, 35% strand | Q6W9E5 |
| D | Polyprotein | protein | 61 | 11% helix, 15% strand | Q91QV1 |
| F | Complement decay-accelerating factor | protein | 252 | 1% helix, 41% strand | P08174 |
Ligands and binding sites
- DAO · Lauric acid · 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 176 | 0.80 | 0.94 | 29 | DAO |
| 2 | 582 | 0.66 | 0.76 | 65 | empty |
| 3 | 76 | 0.57 | 0.87 | 23 | empty |
| 4 | 256 | 0.55 | 0.77 | 32 | empty |
| 5 | 118 | 0.55 | 0.83 | 31 | empty |
Interfaces
9 interfaces between chains.
- A–B · 4397 Ų buried · 68 hydrogen bonds · protein-protein
- A–C · 2075 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 1615 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1179 Ų buried · 15 hydrogen bonds · protein-protein
- C–F · 1011 Ų buried · 52 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 isopeptide (disulfide, isopeptide).
Compared structures
- 3IYP · The Interaction of Decay-accelerating Factor with Echovirus 7 · 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 F against A, TM-score 0.96
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 Q9QP24
- Every structure of UniProt Q6W9E5
- Every structure of UniProt Q91QV1
- Every structure of UniProt P08174
- Elsewhere: RCSB PDB 3IYP · PDBe 3IYP · UniProt Q9QP24 · UniProt Q6W9E5 · UniProt Q91QV1 · UniProt P08174
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