Research workbench
The structure of enterovirus D68 mature virion in complex with Fab 15C5 and 11G1
Analyse The structure of enterovirus D68 mature virion in complex with Fab 15C5 and 11G1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AJ9
- Type
- protein
- Length
- 1,112 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vl of Fab 11G1; Vh of Fab 11G1; Vl of Fab 15C5; Vh of Fab 15C5; Capsid protein VP1…
- UniProt
- A0A097F8Q2, A0A0A7X639
- Pockets
- 13 · best druggability 0.77
Structure
electron microscopy · 7 distinct chains · 4% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Vl of Fab 11G1 | protein | 113 | 0% helix, 32% strand | — |
| D | Vh of Fab 11G1 | protein | 105 | 0% helix, 27% strand | — |
| L | Vl of Fab 15C5 | protein | 97 | 0% helix, 34% strand | — |
| H | Vh of Fab 15C5 | protein | 116 | 3% helix, 39% strand | — |
| A | Capsid protein VP1 | protein | 221 | 6% helix, 29% strand | A0A097F8Q2 |
| B | Capsid protein VP2 | protein | 233 | 5% helix, 24% strand | A0A0A7X639 |
| C | Capsid protein VP3 | protein | 227 | 5% helix, 33% strand | — |
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 194 | 0.77 | 0.92 | 28 | empty |
| 2 | 863 | 0.70 | 0.76 | 83 | empty |
| 3 | 296 | 0.57 | 0.77 | 44 | empty |
| 4 | 163 | 0.56 | 0.81 | 21 | empty |
| 5 | 124 | 0.54 | 0.82 | 17 | empty |
Interfaces
10 interfaces between chains.
- A–C · 2620 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1693 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1679 Ų buried · 11 hydrogen bonds · protein-protein
- L–H · 694 Ų buried · 2 hydrogen bonds · protein-protein
- E–D · 688 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6AJ9 · The structure of Enterovirus D68 mature virion in complex with Fab 15C5 and 11G1 · the same entry in another collection · chain E against E, 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 A0A097F8Q2
- Every structure of UniProt A0A0A7X639
- Elsewhere: RCSB PDB 6AJ9 · PDBe 6AJ9 · UniProt A0A097F8Q2 · UniProt A0A0A7X639
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