Research workbench
Hepatitis E virus E2S domain (genotype I) in complex with a neutralizing antibody
Analyse Hepatitis E virus E2S domain (genotype I) 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
- 3RKD
- Type
- protein
- Length
- 1,153 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein; Monoclonal antibody, light chain; Monoclonal antibody, heavy chain
- UniProt
- B0VX51
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein | protein | 146 | 4% helix, 46% strand | B0VX51 |
| B | Capsid protein | protein | 145 | 4% helix, 46% strand | B0VX51 |
| L, C | Monoclonal antibody, light chain | protein | 213 | 6% helix, 51% strand | — |
| H, D | Monoclonal antibody, heavy chain | protein | 218 | 6% helix, 54% strand | — |
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 548 | 0.72 | 0.81 | 84 | empty |
| 2 | 635 | 0.65 | 0.75 | 72 | empty |
| 3 | 254 | 0.54 | 0.77 | 43 | empty |
| 4 | 90 | 0.53 | 0.85 | 27 | empty |
| 5 | 103 | 0.44 | 0.79 | 22 | empty |
Interfaces
9 interfaces between chains.
- L–H · 1820 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1817 Ų buried · 20 hydrogen bonds · protein-protein
- H–D · 671 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 666 Ų buried · 9 hydrogen bonds · protein-protein
- A–H · 639 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3RKD · Hepatitis E Virus E2s domain (Genotype I) in complex with a neutralizing antibody · 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 B0VX51
- Elsewhere: RCSB PDB 3RKD · PDBe 3RKD · UniProt B0VX51
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