Research workbench
Hepatitis B virus core shell--virus-like particle with NadA epitope
Analyse Hepatitis B virus core shell--virus-like particle with NadA epitope in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TIK
- Type
- protein
- Length
- 550 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.4
- Source
- Hepatitis B virus; Neisseria meningitidis
- Molecule
- Capsid protein,Putative adhesin/invasin,Capsid protein,Factor H-binding protein
- UniProt
- Q67855, D3IRF1, Q6QCC2
- Pockets
- 7 · best druggability 0.69
Structure
electron microscopy · resolution 3.4 · 2 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A | Capsid protein,Putative adhesin/invasin,Capsid protein,Factor H-binding protein | protein | 137 | 72% helix, 0% strand | Q67855, D3IRF1, Q6QCC2 |
| D, B | Capsid protein,Putative adhesin/invasin,Capsid protein,Factor H-binding protein | protein | 138 | 68% helix, 0% strand | Q67855, D3IRF1, Q6QCC2 |
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 222 | 0.69 | 0.85 | 31 | empty |
| 2 | 68 | 0.58 | 0.89 | 18 | empty |
| 3 | 142 | 0.56 | 0.82 | 20 | empty |
| 4 | 114 | 0.54 | 0.83 | 20 | empty |
| 5 | 97 | 0.49 | 0.81 | 19 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2009 Ų buried · 15 hydrogen bonds · protein-protein
- B–A · 1992 Ų buried · 14 hydrogen bonds · protein-protein
- C–B · 606 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6TIK · Hepatitis B virus core shell--virus-like particle with nada epitope · 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 Q67855
- Every structure of UniProt D3IRF1
- Every structure of UniProt Q6QCC2
- Elsewhere: RCSB PDB 6TIK · PDBe 6TIK · UniProt Q67855 · UniProt D3IRF1 · UniProt Q6QCC2
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