Research workbench
Ev-D68 in complex with 8F12 Fab
Analyse Ev-D68 in complex with 8F12 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EC5
- Type
- protein
- Length
- 1,042 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 8F12 Fab light chain; 8F12 Fab heavy chain; Capsid protein VP1; Capsid protein VP3…
- EC
- 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48
- UniProt
- A0A097BW12
- Pockets
- 16 · best druggability 0.78
Structure
electron microscopy · 6 distinct chains · 8% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | 8F12 Fab light chain | protein | 106 | 3% helix, 50% strand | — |
| E | 8F12 Fab heavy chain | protein | 119 | 3% helix, 43% strand | — |
| A | Capsid protein VP1 | protein | 292 | 9% helix, 33% strand | A0A097BW12 |
| C | Capsid protein VP3 | protein | 247 | 10% helix, 29% strand | A0A097BW12 |
| B | Genome polyprotein (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 238 | 10% helix, 38% strand | A0A097BW12 |
| D | Capsid protein VP4 | protein | 40 | 18% helix, 8% strand | A0A097BW12 |
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 536 | 0.78 | 0.85 | 49 | empty |
| 2 | 679 | 0.67 | 0.76 | 68 | empty |
| 3 | 190 | 0.63 | 0.84 | 25 | empty |
| 4 | 258 | 0.56 | 0.77 | 41 | empty |
| 5 | 185 | 0.52 | 0.78 | 25 | empty |
Interfaces
12 interfaces between chains.
- A–C · 4707 Ų buried · 81 hydrogen bonds · protein-protein
- A–B · 2150 Ų buried · 36 hydrogen bonds · protein-protein
- C–B · 1830 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 1190 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 902 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7EC5 · EV-D68 in complex with 8F12 Fab · the same entry in another collection · chain F against F, 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
- Elsewhere: RCSB PDB 7EC5 · PDBe 7EC5 · UniProt A0A097BW12
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