MolNFT v1 · #177269 · protein
Ev-D68 in complex with 2H12 Fab (state 3)
7ECY · Capsid protein VP1: “Ev-D68 in complex with 2H12 Fab (state 3)”. Electron microscopy, 13 pockets (best druggability 0.79). MolNFT v1 #177269 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7ECY
- Type
- protein
- Length
- 876 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1; Capsid protein VP3; Capsid protein VP2; Fab 2H12 heavy chain; Fab…
- UniProt
- A0A097BW12
- Pockets
- 13 · best druggability 0.79
Structure
electron microscopy · 5 distinct chains · 5% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 205 | 6% helix, 35% strand | A0A097BW12 |
| B | Capsid protein VP3 | protein | 221 | 8% helix, 27% strand | A0A097BW12 |
| C | Capsid protein VP2 | protein | 222 | 8% helix, 34% strand | A0A097BW12 |
| E | Fab 2H12 heavy chain | protein | 119 | 0% helix, 29% strand | — |
| F | Fab 2H12 light chain | protein | 109 | 0% helix, 42% strand | — |
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 507 | 0.79 | 0.86 | 67 | empty |
| 2 | 177 | 0.54 | 0.79 | 32 | empty |
| 3 | 160 | 0.54 | 0.80 | 30 | empty |
| 4 | 65 | 0.51 | 0.85 | 19 | empty |
| 5 | 132 | 0.43 | 0.76 | 20 | empty |
Interfaces
8 interfaces between chains.
- A–B · 2210 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1745 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1690 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 893 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 562 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7ECY · EV-D68 in complex with 2H12 Fab (State 3) · the same entry in another collection · chain A against A, 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 7ECY · PDBe 7ECY · UniProt A0A097BW12
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