MolNFT v1 · #177240 · protein
Ev-D68 in complex with 2H12 Fab (state S1)
7EBZ · Capsid protein VP1: “Ev-D68 in complex with 2H12 Fab (state S1)”. Electron microscopy, 18 pockets (best druggability 0.80). MolNFT v1 #177240 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7EBZ
- Type
- protein
- Length
- 1,027 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1; Capsid protein VP3; Capsid protein VP2; Capsid protein VP4; Fab 2H12…
- UniProt
- A0A097BW12
- Pockets
- 18 · best druggability 0.80
Structure
electron microscopy · 6 distinct chains · 9% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 278 | 9% helix, 33% strand | A0A097BW12 |
| C | Capsid protein VP3 | protein | 247 | 9% helix, 31% strand | A0A097BW12 |
| B | Capsid protein VP2 | protein | 239 | 13% helix, 38% strand | A0A097BW12 |
| D | Capsid protein VP4 | protein | 36 | 19% helix, 8% strand | A0A097BW12 |
| E | Fab 2H12 heavy chain | protein | 119 | 8% helix, 41% strand | — |
| F | Fab 2H12 light chain | protein | 108 | 3% helix, 48% strand | — |
Pockets
18 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 553 | 0.80 | 0.86 | 83 | empty |
| 2 | 276 | 0.65 | 0.82 | 51 | empty |
| 3 | 54 | 0.52 | 0.87 | 20 | empty |
| 4 | 146 | 0.51 | 0.79 | 25 | empty |
| 5 | 181 | 0.50 | 0.77 | 32 | empty |
Interfaces
13 interfaces between chains.
- A–C · 4428 Ų buried · 72 hydrogen bonds · protein-protein
- A–B · 2148 Ų buried · 34 hydrogen bonds · protein-protein
- C–B · 1852 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1088 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 908 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7EBZ · EV-D68 in complex with 2H12 Fab (state S1) · 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 7EBZ · PDBe 7EBZ · UniProt A0A097BW12
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