Research workbench
Enterovirus D68 in complex with human monoclonal antibody EV68-228
Analyse Enterovirus D68 in complex with human monoclonal antibody EV68-228 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WDT
- Type
- protein
- Length
- 1,028 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Viral protein 1; Viral protein 2; Viral protein 3; Viral protein 4; EV68-228 heavy chain…
- UniProt
- A0A097BW12, A0A0A7X639, A0A126D252
- Pockets
- 15 · best druggability 0.71
Structure
electron microscopy · 6 distinct chains · 7% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Viral protein 1 | protein | 296 | 7% helix, 31% strand | A0A097BW12 |
| B | Viral protein 2 | protein | 237 | 10% helix, 35% strand | A0A0A7X639 |
| C | Viral protein 3 | protein | 247 | 9% helix, 31% strand | A0A097BW12 |
| D | Viral protein 4 | protein | 28 | 25% helix, 0% strand | A0A126D252 |
| H | EV68-228 heavy chain | protein | 122 | 0% helix, 37% strand | — |
| L | EV68-228 light chain | protein | 98 | 0% helix, 32% strand | — |
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.71 | 0.96 | 21 | empty |
| 2 | 195 | 0.69 | 0.87 | 43 | empty |
| 3 | 270 | 0.68 | 0.84 | 47 | empty |
| 4 | 165 | 0.53 | 0.79 | 34 | empty |
| 5 | 139 | 0.53 | 0.81 | 28 | empty |
Interfaces
12 interfaces between chains.
- A–C · 4672 Ų buried · 72 hydrogen bonds · protein-protein
- A–B · 2079 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 1833 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 926 Ų buried · 14 hydrogen bonds · protein-protein
- H–L · 845 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6WDT · Enterovirus D68 in complex with human monoclonal antibody EV68-228 · the same entry in another collection · chain H against H, 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
- Every structure of UniProt A0A097BW12
- Every structure of UniProt A0A0A7X639
- Every structure of UniProt A0A126D252
- Elsewhere: RCSB PDB 6WDT · PDBe 6WDT · UniProt A0A097BW12 · UniProt A0A0A7X639 · UniProt A0A126D252
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