Research workbench
De novo designed tetrahedral nanoparticle T33_DN2 presenting BG505 sosip trimers
Analyse De novo designed tetrahedral nanoparticle T33_DN2 presenting BG505 sosip trimers in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VL6
- Type
- protein
- Length
- 2,640 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T33_DN2A; T33_DN2B
- Pockets
- 4 · best druggability 0.51
Structure
electron microscopy · 2 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F, G, H, I, J, K, L, M | T33_DN2A | protein | 122 | 78% helix, 0% strand | — |
| B, N, O, P, Q, R, S, T, U, V, W, X | T33_DN2B | protein | 98 | 81% helix, 0% strand | — |
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.51 | 0.83 | 16 | empty |
| 2 | 74 | 0.51 | 0.84 | 17 | empty |
| 3 | 71 | 0.51 | 0.84 | 15 | empty |
| 4 | 81 | 0.51 | 0.83 | 16 | empty |
Interfaces
36 interfaces between chains.
- I–T · 787 Ų buried · 6 hydrogen bonds · protein-protein
- L–W · 787 Ų buried · 6 hydrogen bonds · protein-protein
- C–N · 785 Ų buried · 6 hydrogen bonds · protein-protein
- J–U · 784 Ų buried · 6 hydrogen bonds · protein-protein
- H–S · 784 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6VL6 · De novo designed tetrahedral nanoparticle T33_dn2 presenting BG505 SOSIP trimers · 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
- Elsewhere: RCSB PDB 6VL6 · PDBe 6VL6
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