Research workbench
Hepatitis E virus E2S domain (genotype IV) in complex with a neutralizing antibody 8G12
Analyse Hepatitis E virus E2S domain (genotype IV) in complex with a neutralizing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PLJ
- Type
- protein
- Length
- 1,142 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein; 8G12 light chain; 8G12 heavy chain
- UniProt
- D3VV84
- Pockets
- 12 · best druggability 0.63
Structure
x-ray diffraction · 6 distinct chains · 5% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein | protein | 148 | 2% helix, 49% strand | D3VV84 |
| B | Capsid protein | protein | 147 | 2% helix, 51% strand | D3VV84 |
| L | 8G12 light chain | protein | 212 | 6% helix, 52% strand | — |
| H | 8G12 heavy chain | protein | 218 | 7% helix, 50% strand | — |
| C | 8G12 light chain | protein | 201 | 6% helix, 49% strand | — |
| D | 8G12 heavy chain | protein | 216 | 4% helix, 50% strand | — |
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 571 | 0.63 | 0.75 | 57 | empty |
| 2 | 542 | 0.60 | 0.74 | 54 | empty |
| 3 | 214 | 0.56 | 0.79 | 28 | empty |
| 4 | 199 | 0.54 | 0.79 | 24 | empty |
| 5 | 255 | 0.50 | 0.74 | 45 | empty |
Interfaces
11 interfaces between chains.
- L–H · 1845 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1816 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1232 Ų buried · 14 hydrogen bonds · protein-protein
- A–H · 445 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 431 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4PLJ · Hepatitis E Virus E2s domain (Genotype IV) in complex with a neutralizing antibody 8G12 · 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 D3VV84
- Elsewhere: RCSB PDB 4PLJ · PDBe 4PLJ · UniProt D3VV84
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